ncRNA AND USES THEREOF

ABSTRACT

The present invention relates to compositions and methods for cancer diagnosis, research and therapy, including but not limited to, cancer markers. In particular, the present invention relates to ncRNAs as diagnostic markers and clinical targets for prostate, lung, breast and pancreatic cancer.

This application is a continuation of U.S. patent application Ser. No.13/299,000, filed Nov. 17, 2011, which claims priority to provisionalapplication 61/415,490, filed Nov. 19, 2010, which is hereinincorporated by reference in its entirety.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made with government support under CA069568, CA132874and CA111275 awarded by the National Institutes of Health andW81XWH-09-2-0014 awarded by the Army Medical Research and MaterialCommand. The government has certain rights in the invention.

FIELD OF THE INVENTION

The present invention relates to compositions and methods for cancerdiagnosis, research and therapy, including but not limited to, cancermarkers. In particular, the present invention relates to ncRNAs asdiagnostic markers and clinical targets for prostate, lung, breast andpancreatic cancer.

BACKGROUND OF THE INVENTION

A central aim in cancer research is to identify altered genes that arecausally implicated in oncogenesis. Several types of somatic mutationshave been identified including base substitutions, insertions,deletions, translocations, and chromosomal gains and losses, all ofwhich result in altered activity of an oncogene or tumor suppressorgene. First hypothesized in the early 1900's, there is now compellingevidence for a causal role for chromosomal rearrangements in cancer(Rowley, Nat Rev Cancer 1: 245 (2001)). Recurrent chromosomalaberrations were thought to be primarily characteristic of leukemias,lymphomas, and sarcomas. Epithelial tumors (carcinomas), which are muchmore common and contribute to a relatively large fraction of themorbidity and mortality associated with human cancer, comprise less than1% of the known, disease-specific chromosomal rearrangements (Mitelman,Mutat Res 462: 247 (2000)). While hematological malignancies are oftencharacterized by balanced, disease-specific chromosomal rearrangements,most solid tumors have a plethora of non-specific chromosomalaberrations. It is thought that the karyotypic complexity of solidtumors is due to secondary alterations acquired through cancer evolutionor progression.

Two primary mechanisms of chromosomal rearrangements have beendescribed. In one mechanism, promoter/enhancer elements of one gene arerearranged adjacent to a proto-oncogene, thus causing altered expressionof an oncogenic protein. This type of translocation is exemplified bythe apposition of immunoglobulin (IG) and T-cell receptor (TCR) genes toMYC leading to activation of this oncogene in B- and T-cellmalignancies, respectively (Rabbitts, Nature 372: 143 (1994)). In thesecond mechanism, rearrangement results in the fusion of two genes,which produces a fusion protein that may have a new function or alteredactivity. The prototypic example of this translocation is the BCR-ABLgene fusion in chronic myelogenous leukemia (CML) (Rowley, Nature 243:290 (1973); de Klein et al., Nature 300: 765 (1982)). Importantly, thisfinding led to the rational development of imatinib mesylate (Gleevec),which successfully targets the BCR-ABL kinase (Deininger et al., Blood105: 2640 (2005)). Thus, diagnostic methods that specifically identifyepithelial tumors are needed.

SUMMARY OF THE INVENTION

The present invention relates to compositions and methods for cancerdiagnosis, research and therapy, including but not limited to, cancermarkers. In particular, the present invention relates to ncRNAs asdiagnostic markers and clinical targets for prostate, lung, breast andpancreatic cancer.

Embodiments of the present invention provide compositions, kits, andmethods useful in the detection and screening of prostate cancer.Experiments conducted during the course of development of embodiments ofthe present invention identified upreguation of non-coding RNAs inprostate cancer. Some embodiments of the present invention providecompositions and methods for detecting expression levels of such ncRNAs.Identification of ncRNAs finds use in screening, diagnostic and researchuses.

For example, in some embodiments, the present invention provides amethod of screening for the presence of prostate cancer in a subject,comprising contacting a biological sample from a subject with a reagentfor detecting the level of expression of one or more non-coding RNAs(ncRNA) (e.g., PCAT1, PCAT14, PCAT43 and PCAT 109); and detecting thelevel of expression of the ncRNA in the sample, for example, using an invitro assay, wherein an increased level of expression of the ncRNA inthe sample (e.g., relative to the level in normal prostate cells,increase in level relative to a prior time point, increase relative to apre-established threshold level, etc.) is indicative of prostate cancerin the subject. In some embodiments, the ncRNAs are described by SEQ IDNOs: 1-9. In some embodiments, the sample is tissue, blood, plasma,serum, urine, urine supernatant, urine cell pellet, semen, prostaticsecretions or prostate cells. In some embodiments, the detection iscarried out utilizing a sequencing technique, a nucleic acidhybridization technique, a nucleic acid amplification technique, or animmunoassay. However, the invention is not limited to the techniqueemployed. In some embodiments, the nucleic acid amplification techniqueis polymerase chain reaction, reverse transcription polymerase chainreaction, transcription-mediated amplification, ligase chain reaction,strand displacement amplification or nucleic acid sequence basedamplification. In some embodiments, the prostate cancer is localizedprostate cancer or metastatic prostate cancer. In some embodiments, thereagent is a pair of amplification oligonucleotides or anoligonucleotide probe.

Additional embodiments provide a method of screening for the presence ofprostate cancer in a subject, comprising contacting a biological samplefrom a subject with a reagent for detecting the level of expression oftwo or more (e.g., 10 or more, 25 or more, 50 or more, 100 or more orall 121) non-coding RNAs (ncRNA) selected from, for example, PCAT1,PCAT2, PCAT3, PCAT4, PCAT5, PCAT6, PCAT7, PCAT8, PCAT9, PCAT10, PCAT11,PCAT12, PCAT13, PCAT14, PCAT15, PCAT16, PCAT17, PCAT18, PCAT19, PCAT20,PCAT21, PCAT22, PCAT23, PCAT24, PCAT25, PCAT26, PCAT27, PCAT28, PCAT29,PCAT30, PCAT31, PCAT32, PCAT33, PCAT34, PCAT35, PCAT36, PCAT37, PCAT38,PCAT39, PCAT40, PCAT41, PCAT42, PCAT43, PCAT44, PCAT45, PCAT46, PCAT47,PCAT48, PCAT49, PCAT50, PCAT51, PCAT52, PCAT53, PCAT54, PCAT55, PCAT56,PCAT57, PCAT58, PCAT59, PCAT60, PCAT61, PCAT62, PCAT63, PCAT64, PCAT65,PCAT66, PCAT67, PCAT68, PCAT69, PCAT70, PCAT71, PCAT72, PCAT73, PCAT74,PCAT75, PCAT76, PCAT77, PCAT78, PCAT79, PCAT80, PCAT81, PCAT82, PCAT83,PCAT84, PCAT85, PCAT86, PCAT87, PCAT88, PCAT89, PCAT90, PCAT91, PCAT92,PCAT93, PCAT94, PCAT95, PCAT96, PCAT97, PCAT98, PCAT99, PCAT100,PCAT101, PCAT102, PCAT103, PCAT104, PCAT105, PCAT106, PCAT107, PCAT108,PCAT109, PCAT110, PCAT111, PCAT112, PCAT113, PCAT114, PCAT115, PCAT116,PCAT117, PCAT118, PCAT119, PCAT120, or PCAT121; and detecting the levelof expression of the ncRNA in the sample using an in vitro assay,wherein an increased level of expression of the ncRNA in the samplerelative to the level in normal prostate cells in indicative of prostatecancer in the subject.

Further embodiments of the present invention provide an array,comprising reagents for detecting the level of expression of two or more(e.g., 10 or more, 25 or more, 50 or more, 100 or more or all 121)non-coding RNAs (ncRNA) selected from, for example, PCAT1, PCAT2, PCAT3,PCAT4, PCAT5, PCAT6, PCAT7, PCAT8, PCAT9, PCAT10, PCAT11, PCAT12,PCAT13, PCAT14, PCAT15, PCAT16, PCAT17, PCAT18, PCAT19, PCAT20, PCAT21,PCAT22, PCAT23, PCAT24, PCAT25, PCAT26, PCAT27, PCAT28, PCAT29, PCAT30,PCAT31, PCAT32, PCAT33, PCAT34, PCAT35, PCAT36, PCAT37, PCAT38, PCAT39,PCAT40, PCAT41, PCAT42, PCAT43, PCAT44, PCAT45, PCAT46, PCAT47, PCAT48,PCAT49, PCAT50, PCAT51, PCAT52, PCAT53, PCAT54, PCAT55, PCAT56, PCAT57,PCAT58, PCAT59, PCAT60, PCAT61, PCAT62, PCAT63, PCAT64, PCAT65, PCAT66,PCAT67, PCAT68, PCAT69, PCAT70, PCAT71, PCAT72, PCAT73, PCAT74, PCAT75,PCAT76, PCAT77, PCAT78, PCAT79, PCAT80, PCAT81, PCAT82, PCAT83, PCAT84,PCAT85, PCAT86, PCAT87, PCAT88, PCAT89, PCAT90, PCAT91, PCAT92, PCAT93,PCAT94, PCAT95, PCAT96, PCAT97, PCAT98, PCAT99, PCAT100, PCAT101,PCAT102, PCAT103, PCAT104, PCAT105, PCAT106, PCAT107, PCAT108, PCAT109,PCAT110, PCAT111, PCAT112, PCAT113, PCAT114, PCAT115, PCAT116, PCAT117,PCAT118, PCAT119, PCAT120, or PCAT121. In some embodiments, the reagentis a pair of amplification oligonucleotides or an oligonucleotide probe.

In some embodiments, the present invention provides a method forscreening for the presence of lung cancer in a subject, comprisingcontacting a biological sample from a subject with a reagent fordetecting the level of expression of one or more non-coding RNAs (e.g.,M41 or ENST-75); and detecting the level of expression of the ncRNA inthe sample, for example, using an in vitro assay, wherein an increasedlevel of expression of the ncRNA in the sample (e.g., relative to thelevel in normal lung cells, increase in level relative to a prior timepoint, increase relative to a pre-established threshold level, etc.) isindicative of lung cancer in the subject.

In some embodiments, the present invention provides a method forscreening for the presence of breast cancer in a subject, comprisingcontacting a biological sample from a subject with a reagent fordetecting the level of expression of one or more non-coding RNAs (e.g.,TU0011194, TU0019356, or TU0024146); and detecting the level ofexpression of the ncRNA in the sample, for example, using an in vitroassay, wherein an increased level of expression of the ncRNA in thesample (e.g., relative to the level in normal breast cells, increase inlevel relative to a prior time point, increase relative to apre-established threshold level, etc.) is indicative of breast cancer inthe subject.

In some embodiments, the present invention provides a method forscreening for the presence of pancreatic cancer in a subject, comprisingcontacting a biological sample from a subject with a reagent fordetecting the level of expression of one or more non-coding RNAs (e.g.,TU0009141, TU0062051, or TU0021861); and detecting the level ofexpression of the ncRNA in the sample, for example, using an in vitroassay, wherein an increased level of expression of the ncRNA in thesample (e.g., relative to the level in normal pancreatic cells, increasein level relative to a prior time point, increase relative to apre-established threshold level, etc.) is indicative of pancreaticcancer in the subject.

Additional embodiments are described herein.

DESCRIPTION OF THE FIGURES

FIG. 1 shows that prostate cancer transcriptome sequencing revealsdysregulation of exemplary transcripts identified herein. a. A globaloverview of transcription in prostate cancer. b. A line graph showingthe cumulative fraction of genes that are expressed at a given RPKMlevel. c. Conservation analysis comparing unannotated transcripts toknown genes and intronic controls shows a low but detectable degree ofpurifying selection among intergenic and intronic unannotatedtranscripts. d-g. Intersection plots displaying the fraction ofunannotated transcripts enriched for H3K4me2 (d), H3K4me3 (e), Acetyl-H3(f) or RNA polymerase II (g) at their transcriptional start site (TSS)using ChIP-Seq and RNA-Seq data for the VCaP prostate cancer cancer cellline. h. A heatmap representing differentially expressed transcripts,including novel unannotated transcripts, in prostate cancer.

FIG. 2 shows that unannotated intergenic transcripts differentiateprostate cancer and benign prostate samples. a. A histogram plotting thegenomic distance between an unannotated ncRNA and the nearestprotein-coding gene. b. A Circos plot displaying the location ofannotated transcripts and unannotated transcripts on Chr15q. c. Aheatmap of differentially expressed or outlier unannotated intergenictranscripts clusters benign samples, localized tumors, and metastaticcancers by unsupervised clustering analyses. d. Cancer outlier profileanalysis (COPA) outlier analysis for the prostate cancer transcriptomereveals known outliers (SPINK1, ERG, and ETV1), as well as numerousunannotated transcripts.

FIG. 3 shows validation of tissue-specific prostate cancer-associatednon-coding RNAs. a-c. Quantitative real-time PCR was performed on apanel of prostate and non-prostate samples to measure expression levelsof three nominated non-coding RNAs (ncRNAs), PCAT-43, PCAT-109, andPCAT-14, upregulated in prostate cancer compared to normal prostatetissues. a. PCAT-43 is a 20 kb ncRNA located 40 kb upstream of PMEPA1 onchr20q13.31. b. PCAT-109, located in a large, 0.5 Mb gene desert regionon chr2q31.3 displays widespread transcription in prostate tissues,particularly metastases. c. PCAT-14, a genomic region on chr22q11.23encompassing a human endogenous retrovirus exhibits marked upregulationin prostate tumors but not metastases.

FIG. 4 shows that prostate cancer ncRNAs populate the Chr8q24 genedesert. a. A schematic of the chr8q24 region. b. Comprehensive analysisof the chr8q24 region by RNA-Seq and ChIP-Seq reveals numeroustranscripts supported by histone modifications, such as Acetyl-H3 andH3K4me3, demarcating active chromatin. c. RT-PCR and Sanger sequencingvalidation of the PCAT-1 exon-exon junction. d. The genomic location ofPCAT-1 determined by 5′ and 3′ RACE. Sequence analysis of PCAT-1 showsthat it is a viral long terminal repeat (LTR) promoter splicing to amarniner family transposase that has been bisected by an Alu repeat. e.qPCR on a panel of prostate and non-prostate samples showsprostate-specific expression and upregulation in prostate cancers andmetastases compared to benign prostate samples. f. Four matchedtumor/normal pairs included in the analysis in e. demonstrate somaticupregulation of PCAT-1 in matched cancer samples.

FIG. 5 shows that ncRNAs serve as urine biomarkers for prostate cancer.a-c. Three ncRNAs displaying biomarker status in prostate cancer tissueswere evaluated on a cohort of urine samples from 77 patients withprostate cancer and 31 controls with negative prostate biopsy resultsand absence of the TMPRSS2-ERG fusion transcript. PCA3 (a); PCAT-1 (b);and PCAT-14 (c).

d. Scatter plots demonstrating distinct patient subsets scoringpositively for PCA3, PCAT-1, or PCAT-14 expression. e. A heatmapdisplaying patients positive and negative for several different prostatecancer biomarkers in urine sediment samples. f. A table displaying thestatistical significance of the ncRNA signature. g. A model fornon-coding RNA (ncRNA) activation in prostate cancer.

FIG. 6 shows Ab initio assembly of the prostate cancer transcriptome.(a) Reads were mapped with TopHat and assembled into library-specifictranscriptomes by Cufflinks. (b) Transcripts corresponding to processedpseudogenes were isolated, and the remaining transcripts werecategorized based on overlap with an aggregated set of known geneannotations.

FIG. 7 shows classification tree results for Chromosome 1. The recursiveregression and partitioning trees (rpart) machine learning algorithm wasused to predict expressed transcripts versus background signal.

FIG. 8 shows transcript assembly of known genes. ab initio transcriptassembly on prostate transcriptome sequencing data was used toreconstruct the known prostate transcriptome. a. SPINK1, a biomarker forprostate cancer. b. PRUNE2 with the PCA3 non-coding RNA within itsintronic regions. c. NFKB1. d. COL9A2.

FIG. 9 shows analysis of EST support for exemplary transcripts. ESTsfrom the UCSC database table “Human ESTs” were used to evaluate theamount of overlap between ESTs and novel transcripts. a. A line graphshowing the fraction of genes whose transcripts are supported by aparticular fraction of ESTs. b. A table displaying the number of ESTssupporting each class of transcripts

FIG. 10 shows analysis of coding potential of unannotated transcripts.DNA sequences for each transcript were extracted and searched for openreading frames (ORFs) using the txCdsPredict program from the UCSCsource tool set.

FIG. 11 shows repetitive content of novel transcripts. The percentage ofrepetitive sequences was assessed in all transcripts by calculating thepercentage of repeat masked nucleotides in each sequence.

FIG. 12 shows distinct ChIP-Seq signatures for repeat-associated andnonrepeat novel ncRNAs. Unannotated transcripts were divided into twogroups, repeat-associated and non-repeat, and intersected with ChIP-Seqdata for Acetyl-H3 and H3K4me3, two histone modifications stronglyassociated with transcriptional start sites (TSS), in two prostatecancer cell lines. a. Acetyl-H3 in LNCaP cells. b. H3K4me3 in LNCaPcells. c. Acetyl-H3 in VCaP cells. d. H3K4me3 in VCaP cells.

FIG. 13 shows overlap of unannotated transcripts with ChIP-Seq data inVCaP cells. Previously published ChIP-Seq data for VCaP prostate cancercells were intersected with unannotated prostate cancer transcripts andannotated control genes. a. H3K4me1 b. H3K36me3.

FIG. 14 shows overlap of unannotated transcripts with ChIP-Seq data inLNCaP cells. ChIP-Seq data for LNCaP prostate cancer cells wereintersected with unannotated transcripts and annotated control genes.ncRNAs were divided into intergenic and intronic. a. H3K4me1 b. H3K4me2c. H3K4me3 d. Acetyl-H3 e. H3K36me3 f. RNA polymerase II.

FIG. 15 shows validation of a novel transcript on chromosome 15. a.Coverage maps showing the average expression levels (RPKM) across thebenign, localized tumor, and metastatic samples shows upregulation of anovel transcript downstream of TLE3. b. Several predicted isoforms ofthis transcript were nominated which retained common exons 1 and 2. c.The exon-exon boundary between exons 1 and 2, as well as an internalportion of exon 3, was validated by RT-PCR in prostate cell line models.d. Sanger sequencing of the RT-PCR product confirmed the junction ofexon 1 and exon 2.

FIG. 16 shows clustering of prostate cancer with outliers. Transcriptswith outlier profile scores in the top 10% were clustered usinghierarchical trees.

FIG. 17 shows validation of novel transcripts in prostate cell lines.11/14 unannotated transcripts selected for validation by RT-PCR and qPCRwere confirmed in cell line models. a. RT-PCR gels showing expectedbands for the 11 transcripts that validated. b. Representative qPCRresults using primers selected from a. The primers used in b areindicated by a red asterisk in a.

FIG. 18 shows that PCAT-14 is upregulated by androgen signaling. VCaPand LNCaP cells were treated 5 nM R1881 or vehicle (ethanol) control.

FIG. 19 shows that PCAT-14 is upregulated in matched tumor tissues. Fourmatched tumor-normal patient tissue samples were assayed for PCAT-14expression by qPCR.

FIG. 20 shows analysis of PCAT-14 transcript structure. a.Representative 5′RACE results using a 3′ primer confirms the presence ofthe sense transcript PCAT-14. Predicted novel transcripts are displayedabove the RACE results. b. DNA sequence analysis of PCAT-14 indicatesexpected splice donor sites, splice acceptor sites, and apolyadenylation site.

FIG. 21 shows analysis of PCAT-1 transcript structure. 5′ and 3′ RACEexperiments showed a ncRNA transcript containing two exons.

FIG. 22 shows that knockdown of PCAT-1 does not affect invasion orproliferation of VCaP cells. VCaP cells were transfected withcustom-made siRNAs targeting PCAT-1 or non-targeting controls. a.Knockdown efficiency for four siRNA oligos individually and pooled.b.-d. siRNAs 2-4 were tested for functional effect due to their higherefficiency of knockdown. b. A cell proliferation assay performed with aCoulter counter shows no significant difference in cell proliferationfollowing knockdown of PCAT-1. c. A WST-1 assay indicates no change inVCaP cell viability following PCAT-1 knockdown. d. A transmembraneinvasion assay shows no change in VCaP cell invasiveness followingPCAT-1 knockdown.

FIG. 23 shows transcription of two Alu elements in a CACNA1D intron. a.Coverage maps representing average expression in RPKM in benign samples,localized tumors, and prostate metastases. b. RPKM expression values forthe CACNA1D Alu transcript across the prostate transcriptome sequencingcohort. c. RT-PCR validation of the Alu transcript in cell line models.d. Sanger sequencing confirmation of RT-PCR fragments verifies thepresence of AluSp transcript sequence. e. Raw sequencing data of aportion of the AluSp sequence.

FIG. 24 shows transcription of numerous repeat elements at the SChLAP1locus. a. Coverage maps representing repeat elements transcribed at thechr2q31.3 locus. b. RPKM expression expression values for the LINE-1repeat region on chr2q31.3 across the prostate transcriptome sequencingcohort. c. RTPCR validation of the LINE-1 repetitive element in cellline models. A 402 bp fragment was amplified. d. Sanger sequencing ofthe PCR fragment confirms identity of the LINE-1 amplicon.

FIG. 25 shows a heatmap of repeats clusters prostate cancer samples.Unannotated transcripts that contained repeat elements were used tocluster prostate cancer samples in an unsupervised manner.

FIG. 26 shows that the SChLAP1 locus spans >500 kb. Visualization oftranscriptome sequencing data in the UCSC genome browser indicates thata large, almost 1 Mb section of chromosome 2 is highly activated incancer, contributing to many individual transcripts regulated in acoordinated fashion.

FIG. 27 shows that the SChLAP1 locus is associated with ETS positivetumors. a. Expression of the SChLAP1 locus was assayed by qPCR asdisplay in FIG. 3b on a cohort of 14 benign prostate tissues, 47localized prostate tumors and 10 metastatic prostate cancers. b.Quantification of the SChLAP1 association with ETS status using thethreshold indicated by the blue dotted line in a.

FIG. 28 shows the sequence of PCAT-1 and PCAT-14.

FIG. 29 shows that PCAT-1 expression sensitizes prostate cancer cells totreatment with PARP-1 inhibitors. (a-d) treatment with the PARP1inhibitor olaparib, (e-h) treatment with the PARP1 inhibitor ABT-888.Stable PCAT-1 knockdown in LNCAP prostate cells reduces sensitivity toolaparib (a) and ABT-888 (e). Stable overexpression in Du145 prostatecancer and RWPE benign prostate cells increases sensitivity to olaparib(b,c) and ABT-888 (f,g). Overexpression of PCAT-1 in MCF7 breast cancercells does not recapitulate this effect (d,h).

FIG. 30 shows that PCAT-1 expression sensitizes prostate cancer cells toradiation treatment. (a) Stable PCAT-1 knockdown in LNCAP prostate cellsreduces sensitivity to radiation. (b,c) Stable overexpression in Du145prostate cancer and RWPE benign prostate cells increases sensitivity toradiation. (d). Overexpression of PCAT-1 in MCF7 breast cancer cellsdoes not recapitulate this effect.

FIG. 31 shows that unannotated intergenic transcripts differentiateprostate cancer and benign samples. (a) The genomic location and exonstructure of SChLAP-1. SChLAP-1 is located on chromosome 2 in apreviously unannotated region. (b) The isoform structure of SChLAP-1.(c) Cell fractionation into nuclear and cytoplasmic fractionsdemonstrates that SChLAP-1 is predominantly nuclear in its localization.(d) Expression of SChLAP-1 in a cohort of prostate cancer and benigntissues indicates that SChLAP-1 is a prostate cancer outlier associatedwith cancers.

FIG. 32 shows that SChLAP-1 is required for prostate cancer cellinvasion and proliferation. (a) Prostate and non-prostate cancer celllines were treated with SChLAP-1 siRNAs. (b and c) As in (a), prostateand non-prostate cell lines were assayed for cell proliferationfollowing SChLAP-1 knockdown. (d) The three most abundant isoforms ofSChLAP-1 were cloned and overexpressed in RWPE benign immortalizedprostate cells at levels similar to LNCaP cancer cells. (e) RWPE cellsoverexpressing SChLAP-1 isoforms show an increased ability to invadethrough Matrigel in Boyden chamber assays.

FIG. 33 shows that deletion analysis of SChLAP-1 identifies a regionessential for its function. (a) RWPE cells overexpressing SChLAP-1deletion constructs or full-length isoform #1 were generated as shown inthe schematic of the constructs. (b) RWPE cells overexpressing SChLAP-1deletion construct5 demonstrated an impaired ability to invade throughMatrigel, while the other deletion constructs showed no reduction intheir ability to induce RWPE cell invasion compared to the wild typeSChLAP-1.

FIG. 34 shows detection of prostate cancer RNAs in patient urinesamples. (a-e). (a) PCA3 (b) PCAT-14 (c) PCAT-1 (d) SChLAP-1 (e) PDLIM5

FIG. 35 shows multiplexing urine SChLAP-1 measurements with serum PSAimproves prostate cancer risk stratification.

FIG. 36 shows analysis of the lung cancer transcriptome. (a) 38 lungcell lines were analyzed by RNA-Seq and then lncRNA transcripts werereconstructed. (b) Expression levels of transcripts observed in lungcell lines. (c) An outlier analyses of 13 unannotated transcripts showsthe presence of novel lncRNAs in subtypes of lung cancer cell lines.

FIG. 37 shows discovery of M41 and ENST-75 in lung cancer. (a) Thegenomic location of M41, which resides in an intron of DSCAM. M41 ispoorly conserved across species. (b) qPCR of M41 demonstrates outlierexpression in 15-20% of lung adenocarcinomas as well as high expressionin breast cells. (c) The genomic location of ENST-75, which demonstrateshigh conservation across species. (d) qPCR of ENST-75 showsup-regulation in lung cancer but not breast or prostate cancers. Highexpression is observed in normal testis.

FIG. 38 shows lncRNAs are drivers and biomarkers in lung cancer. (a)Knockdown of ENST-75 in H1299 cells with independent siRNAsachieving >70% knockdown. (b) Knockdown of ENST-75 in H1299 cellsimpairs cell proliferation. Error bars represent s.e.m. (c) ENST-75expression in lung adenocarcinomas stratifies patient overall survival.(d) Serum detection levels of ENST-75 in normal and lung cancerpatients. (e) Average ENST-75 expression in lung cancer patient seracompared to normal patient sera. Error bars represent s.e.m.

FIG. 39 shows nomination of cancer-associated lncRNAs in breast andpancreatic cancer. (a-c) (a) TU0011194 (b) TU0019356 (c) TU0024146 (d-f)Three novel pancreatic cancer lncRNAs nominated from RNA-Seq data. Allshow outlier expression patterns in pancreatic cancer samples but notbenign samples. (d) TU0009141 (e) TU0062051 (f) TU0021861

DEFINITIONS

To facilitate an understanding of the present invention, a number ofterms and phrases are defined below:

As used herein, the terms “detect”, “detecting” or “detection” maydescribe either the general act of discovering or discerning or thespecific observation of a detectably labeled composition.

As used herein, the term “subject” refers to any organisms that arescreened using the diagnostic methods described herein. Such organismspreferably include, but are not limited to, mammals (e.g., murines,simians, equines, bovines, porcines, canines, felines, and the like),and most preferably includes humans.

The term “diagnosed,” as used herein, refers to the recognition of adisease by its signs and symptoms, or genetic analysis, pathologicalanalysis, histological analysis, and the like.

A “subject suspected of having cancer” encompasses an individual who hasreceived an initial diagnosis (e.g., a CT scan showing a mass orincreased PSA level) but for whom the stage of cancer or presence orabsence of ncRNAs indicative of cancer is not known. The term furtherincludes people who once had cancer (e.g., an individual in remission).In some embodiments, “subjects” are control subjects that are suspectedof having cancer or diagnosed with cancer.

As used herein, the term “characterizing cancer in a subject” refers tothe identification of one or more properties of a cancer sample in asubject, including but not limited to, the presence of benign,pre-cancerous or cancerous tissue, the stage of the cancer, and thesubject's prognosis. Cancers may be characterized by the identificationof the expression of one or more cancer marker genes, including but notlimited to, the ncRNAs disclosed herein.

As used herein, the term “characterizing prostate tissue in a subject”refers to the identification of one or more properties of a prostatetissue sample (e.g., including but not limited to, the presence ofcancerous tissue, the presence or absence of ncRNAs, the presence ofpre-cancerous tissue that is likely to become cancerous, and thepresence of cancerous tissue that is likely to metastasize). In someembodiments, tissues are characterized by the identification of theexpression of one or more cancer marker genes, including but not limitedto, the cancer markers disclosed herein.

As used herein, the term “stage of cancer” refers to a qualitative orquantitative assessment of the level of advancement of a cancer.Criteria used to determine the stage of a cancer include, but are notlimited to, the size of the tumor and the extent of metastases (e.g.,localized or distant).

As used herein, the term “nucleic acid molecule” refers to any nucleicacid containing molecule, including but not limited to, DNA or RNA. Theterm encompasses sequences that include any of the known base analogs ofDNA and RNA including, but not limited to, 4-acetylcytosine,8-hydroxy-N6-methyladenosine, aziridinylcytosine, pseudoisocytosine,5-(carboxyhydroxylmethyl) uracil, 5-fluorouracil, 5-bromouracil,5-carboxymethylaminomethyl-2-thiouracil,5-carboxymethylaminomethyluracil, dihydrouracil, inosine,N6-isopentenyladenine, 1-methyladenine, 1-methylpseudouracil,1-methylguanine, 1-methylinosine, 2,2-dimethylguanine, 2-methyladenine,2-methylguanine, 3-methyl cytosine, 5-methylcytosine, N6-methyladenine,7-methylguanine, 5-methylaminomethyluracil,5-methoxy-aminomethyl-2-thiouracil, beta-D-mannosylqueosine,5′-methoxycarbonylmethyluracil, 5-methoxyuracil,2-methylthio-N6-isopentenyladenine, uracil-5-oxyacetic acid methylester,uracil-5-oxyacetic acid, oxybutoxosine, pseudouracil, queosine,2-thiocytosine, 5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil,5-methyluracil, N-uracil-5-oxyacetic acid methylester,uracil-5-oxyacetic acid, pseudouracil, queosine, 2-thiocytosine, and2,6-diaminopurine.

The term “gene” refers to a nucleic acid (e.g., DNA) sequence thatcomprises coding sequences necessary for the production of apolypeptide, precursor, or RNA (e.g., rRNA, tRNA). The polypeptide canbe encoded by a full length coding sequence or by any portion of thecoding sequence so long as the desired activity or functional properties(e.g., enzymatic activity, ligand binding, signal transduction,immunogenicity, etc.) of the full-length or fragments are retained. Theterm also encompasses the coding region of a structural gene and thesequences located adjacent to the coding region on both the 5′ and 3′ends for a distance of about 1 kb or more on either end such that thegene corresponds to the length of the full-length mRNA. Sequenceslocated 5′ of the coding region and present on the mRNA are referred toas 5′ non-translated sequences. Sequences located 3′ or downstream ofthe coding region and present on the mRNA are referred to as 3′non-translated sequences. The term “gene” encompasses both cDNA andgenomic forms of a gene. A genomic form or clone of a gene contains thecoding region interrupted with non-coding sequences termed “introns” or“intervening regions” or “intervening sequences.” Introns are segmentsof a gene that are transcribed into nuclear RNA (hnRNA); introns maycontain regulatory elements such as enhancers. Introns are removed or“spliced out” from the nuclear or primary transcript; introns thereforeare absent in the messenger RNA (mRNA) transcript. The mRNA functionsduring translation to specify the sequence or order of amino acids in anascent polypeptide.

As used herein, the term “oligonucleotide,” refers to a short length ofsingle-stranded polynucleotide chain. Oligonucleotides are typicallyless than 200 residues long (e.g., between 15 and 100), however, as usedherein, the term is also intended to encompass longer polynucleotidechains. Oligonucleotides are often referred to by their length. Forexample a 24 residue oligonucleotide is referred to as a “24-mer”.Oligonucleotides can form secondary and tertiary structures byself-hybridizing or by hybridizing to other polynucleotides. Suchstructures can include, but are not limited to, duplexes, hairpins,cruciforms, bends, and triplexes.

As used herein, the terms “complementary” or “complementarity” are usedin reference to polynucleotides (i.e., a sequence of nucleotides)related by the base-pairing rules. For example, the sequence“5′-A-G-T-3′,” is complementary to the sequence “3′-T-C-A-5′.”Complementarity may be “partial,” in which only some of the nucleicacids' bases are matched according to the base pairing rules. Or, theremay be “complete” or “total” complementarity between the nucleic acids.The degree of complementarity between nucleic acid strands hassignificant effects on the efficiency and strength of hybridizationbetween nucleic acid strands. This is of particular importance inamplification reactions, as well as detection methods that depend uponbinding between nucleic acids.

The term “homology” refers to a degree of complementarity. There may bepartial homology or complete homology (i.e., identity). A partiallycomplementary sequence is a nucleic acid molecule that at leastpartially inhibits a completely complementary nucleic acid molecule fromhybridizing to a target nucleic acid is “substantially homologous.” Theinhibition of hybridization of the completely complementary sequence tothe target sequence may be examined using a hybridization assay(Southern or Northern blot, solution hybridization and the like) underconditions of low stringency. A substantially homologous sequence orprobe will compete for and inhibit the binding (i.e., the hybridization)of a completely homologous nucleic acid molecule to a target underconditions of low stringency. This is not to say that conditions of lowstringency are such that non-specific binding is permitted; lowstringency conditions require that the binding of two sequences to oneanother be a specific (i.e., selective) interaction. The absence ofnon-specific binding may be tested by the use of a second target that issubstantially non-complementary (e.g., less than about 30% identity); inthe absence of non-specific binding the probe will not hybridize to thesecond non-complementary target.

As used herein, the term “hybridization” is used in reference to thepairing of complementary nucleic acids. Hybridization and the strengthof hybridization (i.e., the strength of the association between thenucleic acids) is impacted by such factors as the degree ofcomplementary between the nucleic acids, stringency of the conditionsinvolved, the T_(m) of the formed hybrid, and the G:C ratio within thenucleic acids. A single molecule that contains pairing of complementarynucleic acids within its structure is said to be “self-hybridized.”

As used herein the term “stringency” is used in reference to theconditions of temperature, ionic strength, and the presence of othercompounds such as organic solvents, under which nucleic acidhybridizations are conducted. Under “low stringency conditions” anucleic acid sequence of interest will hybridize to its exactcomplement, sequences with single base mismatches, closely relatedsequences (e.g., sequences with 90% or greater homology), and sequenceshaving only partial homology (e.g., sequences with 50-90% homology).Under ‘medium stringency conditions,” a nucleic acid sequence ofinterest will hybridize only to its exact complement, sequences withsingle base mismatches, and closely relation sequences (e.g., 90% orgreater homology). Under “high stringency conditions,” a nucleic acidsequence of interest will hybridize only to its exact complement, and(depending on conditions such a temperature) sequences with single basemismatches. In other words, under conditions of high stringency thetemperature can be raised so as to exclude hybridization to sequenceswith single base mismatches.

The term “isolated” when used in relation to a nucleic acid, as in “anisolated oligonucleotide” or “isolated polynucleotide” refers to anucleic acid sequence that is identified and separated from at least onecomponent or contaminant with which it is ordinarily associated in itsnatural source. Isolated nucleic acid is such present in a form orsetting that is different from that in which it is found in nature. Incontrast, non-isolated nucleic acids as nucleic acids such as DNA andRNA found in the state they exist in nature. For example, a given DNAsequence (e.g., a gene) is found on the host cell chromosome inproximity to neighboring genes; RNA sequences, such as a specific mRNAsequence encoding a specific protein, are found in the cell as a mixturewith numerous other mRNAs that encode a multitude of proteins. However,isolated nucleic acid encoding a given protein includes, by way ofexample, such nucleic acid in cells ordinarily expressing the givenprotein where the nucleic acid is in a chromosomal location differentfrom that of natural cells, or is otherwise flanked by a differentnucleic acid sequence than that found in nature. The isolated nucleicacid, oligonucleotide, or polynucleotide may be present insingle-stranded or double-stranded form. When an isolated nucleic acid,oligonucleotide or polynucleotide is to be utilized to express aprotein, the oligonucleotide or polynucleotide will contain at a minimumthe sense or coding strand (i.e., the oligonucleotide or polynucleotidemay be single-stranded), but may contain both the sense and anti-sensestrands (i.e., the oligonucleotide or polynucleotide may bedouble-stranded).

As used herein, the term “purified” or “to purify” refers to the removalof components (e.g., contaminants) from a sample. For example,antibodies are purified by removal of contaminating non-immunoglobulinproteins; they are also purified by the removal of immunoglobulin thatdoes not bind to the target molecule. The removal of non-immunoglobulinproteins and/or the removal of immunoglobulins that do not bind to thetarget molecule results in an increase in the percent of target-reactiveimmunoglobulins in the sample. In another example, recombinantpolypeptides are expressed in bacterial host cells and the polypeptidesare purified by the removal of host cell proteins; the percent ofrecombinant polypeptides is thereby increased in the sample.

As used herein, the term “sample” is used in its broadest sense. In onesense, it is meant to include a specimen or culture obtained from anysource, as well as biological and environmental samples. Biologicalsamples may be obtained from animals (including humans) and encompassfluids, solids, tissues, and gases. Biological samples include bloodproducts, such as plasma, serum and the like. Such examples are nothowever to be construed as limiting the sample types applicable to thepresent invention.

DETAILED DESCRIPTION OF THE INVENTION

The present invention relates to compositions and methods for cancerdiagnosis, research and therapy, including but not limited to, cancermarkers. In particular, the present invention relates to ncRNAs asdiagnostic markers and clinical targets for prostate, lung, breast andpancreatic cancer.

Experiments conducted during the development of embodiments of thepresent invention utilized RNA-Seq analyses of tissue samples and abinitio transcriptome assembly to predict the complete polyA+transcriptome of prostate cancer. 6,144 novel ncRNAs found in prostatecancer were identified, including 121 ncRNAs that associated withdisease progression (FIGS. 1, 2, 16 and 25). These data demonstrate theglobal utility of RNA-Seq in defining functionally-important elements ofthe genome.

The present invention is not limited to a particular mechanism. Indeed,an understanding of the mechanism is not necessary to practice thepresent invention. Nonetheless, although the biological role of theseRNAs, especially the differentially-expressed ones, is not yet known,these results indicate a model in which specific intergenic loci areactivated in prostate cancer, enabling the transcription of numerousdisease-specific and tissue-specific ncRNAs (FIG. 5g ). Clinically,these ncRNA signatures are suitable for urine-based assays to detect anddiagnose prostate cancer in a non-invasive manner (See e.g., Example 1).It is further contemplated that specific ncRNA signatures occuruniversally in all disease states and applying these methodologies toother diseases reveals clinically important biomarkers, particularly fordiseases that currently lack good protein biomarkers.

While traditional approaches have focused on the annotated referencegenome, data generated during the course of development of embodimentsof the present invention implicate large swaths of unannotated genomicloci in prostate cancer progression and prostate-specific expression.One example of this is the SChLAP1 locus, which represents a >500 kbstretch of coordinately regulated expression, and the chr8q24 locus,which contains a prostate specific region with the prostate cancerbiomarker PCAT-1. The fact that the SChLAP1 locus is almost exclusivelyexpressed in prostate cancers harboring an ETS gene fusion furtherconfirms the capacity of ncRNAs to identify patient disease subtypes. Inaddition, these analyses reveal novel cancer-specific drivers oftumorigenesis. For example, the long ncRNA HOTAIR is known to directcancer-promoting roles for EZH2 in breast cancer (Gupta et al., Nature464 (7291), 1071 (2010)), while in the PC3 prostate cancer cell line asimilar role has been proposed for the ANRIL ncRNA (Yap et al., Mol Cell38 (5), 662 (2010)).

I. Diagnostic and Screening Methods

As described above, embodiments of the present invention providediagnostic and screening methods that utilize the detection of ncRNAs(e.g., PCAT-1, PCAT-14, PCAT-43 and PCAT-109; SEQ ID NOs: 1-9).Exemplary, non-limiting methods are described below.

Any patient sample suspected of containing the ncRNAs may be testedaccording to methods of embodiments of the present invention. By way ofnon-limiting examples, the sample may be tissue (e.g., a prostate biopsysample or a tissue sample obtained by prostatectomy), blood, urine,semen, prostatic secretions or a fraction thereof (e.g., plasma, serum,urine supernatant, urine cell pellet or prostate cells). A urine sampleis preferably collected immediately following an attentive digitalrectal examination (DRE), which causes prostate cells from the prostategland to shed into the urinary tract.

In some embodiments, the patient sample is subjected to preliminaryprocessing designed to isolate or enrich the sample for the ncRNAs orcells that contain the ncRNAs. A variety of techniques known to those ofordinary skill in the art may be used for this purpose, including butnot limited to: centrifugation; immunocapture; cell lysis; and, nucleicacid target capture (See, e.g., EP Pat. No. 1 409 727, hereinincorporated by reference in its entirety).

The ncRNAs may be detected along with other markers in a multiplex orpanel format. Markers are selected for their predictive value alone orin combination with the gene fusions. Exemplary prostate cancer markersinclude, but are not limited to: AMACR/P504S (U.S. Pat. No. 6,262,245);PCA3 (U.S. Pat. No. 7,008,765); PCGEM1 (U.S. Pat. No. 6,828,429);prostein/P501S, P503S, P504S, P509S, P510S, prostase/P703P, P710P (U.S.Publication No. 20030185830); RAS/KRAS (Bos, Cancer Res. 49:4682-89(1989); Kranenburg, Biochimica et Biophysica Acta 1756:81-82 (2005));and, those disclosed in U.S. Pat. Nos. 5,854,206 and 6,034,218,7,229,774, each of which is herein incorporated by reference in itsentirety. Markers for other cancers, diseases, infections, and metabolicconditions are also contemplated for inclusion in a multiplex or panelformat.

In some embodiments, multiplex or array formats are utilized to detectedmultiple markers in combination. For example, in some embodiments, thelevel of expression of two or more (e.g., 10 or more, 25 or more, 50 ormore, 100 or more or all 121) non-coding RNAs (ncRNA) selected from, forexample, PCAT1, PCAT2, PCAT3, PCAT4, PCAT5, PCAT6, PCAT7, PCAT8, PCAT9,PCAT10, PCAT11, PCAT12, PCAT13, PCAT14, PCAT15, PCAT16, PCAT17, PCAT18,PCAT19, PCAT20, PCAT21, PCAT22, PCAT23, PCAT24, PCAT25, PCAT26, PCAT27,PCAT28, PCAT29, PCAT30, PCAT31, PCAT32, PCAT33, PCAT34, PCAT35, PCAT36,PCAT37, PCAT38, PCAT39, PCAT40, PCAT41, PCAT42, PCAT43, PCAT44, PCAT45,PCAT46, PCAT47, PCAT48, PCAT49, PCAT50, PCAT51, PCAT52, PCAT53, PCAT54,PCAT55, PCAT56, PCAT57, PCAT58, PCAT59, PCAT60, PCAT61, PCAT62, PCAT63,PCAT64, PCAT65, PCAT66, PCAT67, PCAT68, PCAT69, PCAT70, PCAT71, PCAT72,PCAT73, PCAT74, PCAT75, PCAT76, PCAT77, PCAT78, PCAT79, PCAT80, PCAT81,PCAT82, PCAT83, PCAT84, PCAT85, PCAT86, PCAT87, PCAT88, PCAT89, PCAT90,PCAT91, PCAT92, PCAT93, PCAT94, PCAT95, PCAT96, PCAT97, PCAT98, PCAT99,PCAT100, PCAT101, PCAT102, PCAT103, PCAT104, PCAT105, PCAT106, PCAT107,PCAT108, PCAT109, PCAT110, PCAT111, PCAT112, PCAT113, PCAT114, PCAT115,PCAT116, PCAT117, PCAT118, PCAT119, PCAT120, or PCAT121 is utilized inthe research, screening, diagnostic and prognositic compositions andmethods described herein.

i. DNA and RNA Detection

The ncRNAs of the present invention are detected using a variety ofnucleic acid techniques known to those of ordinary skill in the art,including but not limited to: nucleic acid sequencing; nucleic acidhybridization; and, nucleic acid amplification.

1. Sequencing

Illustrative non-limiting examples of nucleic acid sequencing techniquesinclude, but are not limited to, chain terminator (Sanger) sequencingand dye terminator sequencing. Those of ordinary skill in the art willrecognize that because RNA is less stable in the cell and more prone tonuclease attack experimentally RNA is usually reverse transcribed to DNAbefore sequencing.

Chain terminator sequencing uses sequence-specific termination of a DNAsynthesis reaction using modified nucleotide substrates. Extension isinitiated at a specific site on the template DNA by using a shortradioactive, or other labeled, oligonucleotide primer complementary tothe template at that region. The oligonucleotide primer is extendedusing a DNA polymerase, standard four deoxynucleotide bases, and a lowconcentration of one chain terminating nucleotide, most commonly adi-deoxynucleotide. This reaction is repeated in four separate tubeswith each of the bases taking turns as the di-deoxynucleotide. Limitedincorporation of the chain terminating nucleotide by the DNA polymeraseresults in a series of related DNA fragments that are terminated only atpositions where that particular di-deoxynucleotide is used. For eachreaction tube, the fragments are size-separated by electrophoresis in aslab polyacrylamide gel or a capillary tube filled with a viscouspolymer. The sequence is determined by reading which lane produces avisualized mark from the labeled primer as you scan from the top of thegel to the bottom.

Dye terminator sequencing alternatively labels the terminators. Completesequencing can be performed in a single reaction by labeling each of thedi-deoxynucleotide chain-terminators with a separate fluorescent dye,which fluoresces at a different wavelength.

A variety of nucleic acid sequencing methods are contemplated for use inthe methods of the present disclosure including, for example, chainterminator (Sanger) sequencing, dye terminator sequencing, andhigh-throughput sequencing methods. Many of these sequencing methods arewell known in the art. See, e.g., Sanger et al., Proc. Natl. Acad. Sci.USA 74:5463-5467 (1997); Maxam et al., Proc. Natl. Acad. Sci. USA74:560-564 (1977); Drmanac, et al., Nat. Biotechnol. 16:54-58 (1998);Kato, Int. J. Clin. Exp. Med. 2:193-202 (2009); Ronaghi et al., Anal.Biochem. 242:84-89 (1996); Margulies et al., Nature 437:376-380 (2005);Ruparel et al., Proc. Natl. Acad. Sci. USA 102:5932-5937 (2005), andHarris et al., Science 320:106-109 (2008); Levene et al., Science299:682-686 (2003); Korlach et al., Proc. Natl. Acad. Sci. USA105:1176-1181 (2008); Branton et al., Nat. Biotechnol. 26(10):1146-53(2008); Eid et al., Science 323:133-138 (2009); each of which is hereinincorporated by reference in its entirety.

2. Hybridization

Illustrative non-limiting examples of nucleic acid hybridizationtechniques include, but are not limited to, in situ hybridization (ISH),microarray, and Southern or Northern blot. In situ hybridization (ISH)is a type of hybridization that uses a labeled complementary DNA or RNAstrand as a probe to localize a specific DNA or RNA sequence in aportion or section of tissue (in situ), or, if the tissue is smallenough, the entire tissue (whole mount ISH). DNA ISH can be used todetermine the structure of chromosomes. RNA ISH is used to measure andlocalize mRNAs and other transcripts (e.g., ncRNAs) within tissuesections or whole mounts. Sample cells and tissues are usually treatedto fix the target transcripts in place and to increase access of theprobe. The probe hybridizes to the target sequence at elevatedtemperature, and then the excess probe is washed away. The probe thatwas labeled with either radio-, fluorescent- or antigen-labeled bases islocalized and quantitated in the tissue using either autoradiography,fluorescence microscopy or immunohistochemistry, respectively. ISH canalso use two or more probes, labeled with radioactivity or the othernon-radioactive labels, to simultaneously detect two or moretranscripts.

In some embodiments, ncRNAs are detected using fluorescence in situhybridization (FISH). In some embodiments, FISH assays utilize bacterialartificial chromosomes (BACs). These have been used extensively in thehuman genome sequencing project (see Nature 409: 953-958 (2001)) andclones containing specific BACs are available through distributors thatcan be located through many sources, e.g., NCBI. Each BAC clone from thehuman genome has been given a reference name that unambiguouslyidentifies it. These names can be used to find a corresponding GenBanksequence and to order copies of the clone from a distributor.

The present invention further provides a method of performing a FISHassay on human prostate cells, human prostate tissue or on the fluidsurrounding said human prostate cells or human prostate tissue. Specificprotocols are well known in the art and can be readily adapted for thepresent invention. Guidance regarding methodology may be obtained frommany references including: In situ Hybridization: Medical Applications(eds. G. R. Coulton and J. de Belleroche), Kluwer Academic Publishers,Boston (1992); In situ Hybridization: In Neurobiology; Advances inMethodology (eds. J. H. Eberwine, K. L. Valentino, and J. D. Barchas),Oxford University Press Inc., England (1994); In situ Hybridization: APractical Approach (ed. D. G. Wilkinson), Oxford University Press Inc.,England (1992)); Kuo, et al., Am. J. Hum. Genet. 49:112-119 (1991);Klinger, et al., Am. J. Hum. Genet. 51:55-65 (1992); and Ward, et al.,Am. J. Hum. Genet. 52:854-865 (1993)). There are also kits that arecommercially available and that provide protocols for performing FISHassays (available from e.g., Oncor, Inc., Gaithersburg, Md.). Patentsproviding guidance on methodology include U.S. Pat. No. 5,225,326;5,545,524; 6,121,489 and 6,573,043. All of these references are herebyincorporated by reference in their entirety and may be used along withsimilar references in the art and with the information provided in theExamples section herein to establish procedural steps convenient for aparticular laboratory.

3. Microarrays

Different kinds of biological assays are called microarrays including,but not limited to: DNA microarrays (e.g., cDNA microarrays andoligonucleotide microarrays); protein microarrays; tissue microarrays;transfection or cell microarrays; chemical compound microarrays; and,antibody microarrays. A DNA microarray, commonly known as gene chip, DNAchip, or biochip, is a collection of microscopic DNA spots attached to asolid surface (e.g., glass, plastic or silicon chip) forming an arrayfor the purpose of expression profiling or monitoring expression levelsfor thousands of genes simultaneously. The affixed DNA segments areknown as probes, thousands of which can be used in a single DNAmicroarray. Microarrays can be used to identify disease genes ortranscripts (e.g., ncRNAs) by comparing gene expression in disease andnormal cells. Microarrays can be fabricated using a variety oftechnologies, including but not limiting: printing with fine-pointedpins onto glass slides; photolithography using pre-made masks;photolithography using dynamic micromirror devices; ink-jet printing;or, electrochemistry on microelectrode arrays.

Southern and Northern blotting is used to detect specific DNA or RNAsequences, respectively. DNA or RNA extracted from a sample isfragmented, electrophoretically separated on a matrix gel, andtransferred to a membrane filter. The filter bound DNA or RNA is subjectto hybridization with a labeled probe complementary to the sequence ofinterest. Hybridized probe bound to the filter is detected. A variant ofthe procedure is the reverse Northern blot, in which the substratenucleic acid that is affixed to the membrane is a collection of isolatedDNA fragments and the probe is RNA extracted from a tissue and labeled.

3. Amplification

Nucleic acids (e.g., ncRNAs) may be amplified prior to or simultaneouswith detection. Illustrative non-limiting examples of nucleic acidamplification techniques include, but are not limited to, polymerasechain reaction (PCR), reverse transcription polymerase chain reaction(RT-PCR), transcription-mediated amplification (TMA), ligase chainreaction (LCR), strand displacement amplification (SDA), and nucleicacid sequence based amplification (NASBA). Those of ordinary skill inthe art will recognize that certain amplification techniques (e.g., PCR)require that RNA be reversed transcribed to DNA prior to amplification(e.g., RT-PCR), whereas other amplification techniques directly amplifyRNA (e.g., TMA and NASBA).

The polymerase chain reaction (U.S. Pat. Nos. 4,683,195, 4,683,202,4,800,159 and 4,965,188, each of which is herein incorporated byreference in its entirety), commonly referred to as PCR, uses multiplecycles of denaturation, annealing of primer pairs to opposite strands,and primer extension to exponentially increase copy numbers of a targetnucleic acid sequence. In a variation called RT-PCR, reversetranscriptase (RT) is used to make a complementary DNA (cDNA) from mRNA,and the cDNA is then amplified by PCR to produce multiple copies of DNA.For other various permutations of PCR see, e.g., U.S. Pat. Nos.4,683,195, 4,683,202 and 4,800,159; Mullis et al., Meth. Enzymol. 155:335 (1987); and, Murakawa et al., DNA 7: 287 (1988), each of which isherein incorporated by reference in its entirety.

Transcription mediated amplification (U.S. Pat. Nos. 5,480,784 and5,399,491, each of which is herein incorporated by reference in itsentirety), commonly referred to as TMA, synthesizes multiple copies of atarget nucleic acid sequence autocatalytically under conditions ofsubstantially constant temperature, ionic strength, and pH in whichmultiple RNA copies of the target sequence autocatalytically generateadditional copies. See, e.g., U.S. Pat. Nos. 5,399,491 and 5,824,518,each of which is herein incorporated by reference in its entirety. In avariation described in U.S. Publ. No. 20060046265 (herein incorporatedby reference in its entirety), TMA optionally incorporates the use ofblocking moieties, terminating moieties, and other modifying moieties toimprove TMA process sensitivity and accuracy.

The ligase chain reaction (Weiss, R., Science 254: 1292 (1991), hereinincorporated by reference in its entirety), commonly referred to as LCR,uses two sets of complementary DNA oligonucleotides that hybridize toadjacent regions of the target nucleic acid. The DNA oligonucleotidesare covalently linked by a DNA ligase in repeated cycles of thermaldenaturation, hybridization and ligation to produce a detectabledouble-stranded ligated oligonucleotide product.

Strand displacement amplification (Walker, G. et al., Proc. Natl. Acad.Sci. USA 89: 392-396 (1992); U.S. Pat. Nos. 5,270,184 and 5,455,166,each of which is herein incorporated by reference in its entirety),commonly referred to as SDA, uses cycles of annealing pairs of primersequences to opposite strands of a target sequence, primer extension inthe presence of a dNTPaS to produce a duplex hemiphosphorothioatedprimer extension product, endonuclease-mediated nicking of ahemimodified restriction endonuclease recognition site, andpolymerase-mediated primer extension from the 3′ end of the nick todisplace an existing strand and produce a strand for the next round ofprimer annealing, nicking and strand displacement, resulting ingeometric amplification of product. Thermophilic SDA (tSDA) usesthermophilic endonucleases and polymerases at higher temperatures inessentially the same method (EP Pat. No. 0 684 315).

Other amplification methods include, for example: nucleic acid sequencebased amplification (U.S. Pat. No. 5,130,238, herein incorporated byreference in its entirety), commonly referred to as NASBA; one that usesan RNA replicase to amplify the probe molecule itself (Lizardi et al.,BioTechnol. 6: 1197 (1988), herein incorporated by reference in itsentirety), commonly referred to as Qβ replicase; a transcription basedamplification method (Kwoh et al., Proc. Natl. Acad. Sci. USA 86:1173(1989)); and, self-sustained sequence replication (Guatelli et al.,Proc. Natl. Acad. Sci. USA 87: 1874 (1990), each of which is hereinincorporated by reference in its entirety). For further discussion ofknown amplification methods see Persing, David H., “In Vitro NucleicAcid Amplification Techniques” in Diagnostic Medical Microbiology:Principles and Applications (Persing et al., Eds.), pp. 51-87 (AmericanSociety for Microbiology, Washington, D.C. (1993)).

4. Detection Methods

Non-amplified or amplified nucleic acids can be detected by anyconventional means. For example, the ncRNAs can be detected byhybridization with a detectably labeled probe and measurement of theresulting hybrids. Illustrative non-limiting examples of detectionmethods are described below.

One illustrative detection method, the Hybridization Protection Assay(HPA) involves hybridizing a chemiluminescent oligonucleotide probe(e.g., an acridinium ester-labeled (AE) probe) to the target sequence,selectively hydrolyzing the chemiluminescent label present onunhybridized probe, and measuring the chemiluminescence produced fromthe remaining probe in a luminometer. See, e.g., U.S. Pat. No. 5,283,174and Norman C. Nelson et al., Nonisotopic Probing, Blotting, andSequencing, ch. 17 (Larry J. Kricka ed., 2d ed. 1995, each of which isherein incorporated by reference in its entirety).

Another illustrative detection method provides for quantitativeevaluation of the amplification process in real-time. Evaluation of anamplification process in “real-time” involves determining the amount ofamplicon in the reaction mixture either continuously or periodicallyduring the amplification reaction, and using the determined values tocalculate the amount of target sequence initially present in the sample.A variety of methods for determining the amount of initial targetsequence present in a sample based on real-time amplification are wellknown in the art. These include methods disclosed in U.S. Pat. Nos.6,303,305 and 6,541,205, each of which is herein incorporated byreference in its entirety. Another method for determining the quantityof target sequence initially present in a sample, but which is not basedon a real-time amplification, is disclosed in U.S. Pat. No. 5,710,029,herein incorporated by reference in its entirety.

Amplification products may be detected in real-time through the use ofvarious self-hybridizing probes, most of which have a stem-loopstructure. Such self-hybridizing probes are labeled so that they emitdifferently detectable signals, depending on whether the probes are in aself-hybridized state or an altered state through hybridization to atarget sequence. By way of non-limiting example, “molecular torches” area type of self-hybridizing probe that includes distinct regions ofself-complementarity (referred to as “the target binding domain” and“the target closing domain”) which are connected by a joining region(e.g., non-nucleotide linker) and which hybridize to each other underpredetermined hybridization assay conditions. In a preferred embodiment,molecular torches contain single-stranded base regions in the targetbinding domain that are from 1 to about 20 bases in length and areaccessible for hybridization to a target sequence present in anamplification reaction under strand displacement conditions. Understrand displacement conditions, hybridization of the two complementaryregions, which may be fully or partially complementary, of the moleculartorch is favored, except in the presence of the target sequence, whichwill bind to the single-stranded region present in the target bindingdomain and displace all or a portion of the target closing domain. Thetarget binding domain and the target closing domain of a molecular torchinclude a detectable label or a pair of interacting labels (e.g.,luminescent/quencher) positioned so that a different signal is producedwhen the molecular torch is self-hybridized than when the moleculartorch is hybridized to the target sequence, thereby permitting detectionof probe:target duplexes in a test sample in the presence ofunhybridized molecular torches. Molecular torches and a variety of typesof interacting label pairs are disclosed in U.S. Pat. No. 6,534,274,herein incorporated by reference in its entirety.

Another example of a detection probe having self-complementarity is a“molecular beacon.” Molecular beacons include nucleic acid moleculeshaving a target complementary sequence, an affinity pair (or nucleicacid arms) holding the probe in a closed conformation in the absence ofa target sequence present in an amplification reaction, and a label pairthat interacts when the probe is in a closed conformation. Hybridizationof the target sequence and the target complementary sequence separatesthe members of the affinity pair, thereby shifting the probe to an openconformation. The shift to the open conformation is detectable due toreduced interaction of the label pair, which may be, for example, afluorophore and a quencher (e.g., DABCYL and EDANS). Molecular beaconsare disclosed in U.S. Pat. Nos. 5,925,517 and 6,150,097, hereinincorporated by reference in its entirety.

Other self-hybridizing probes are well known to those of ordinary skillin the art. By way of non-limiting example, probe binding pairs havinginteracting labels, such as those disclosed in U.S. Pat. No. 5,928,862(herein incorporated by reference in its entirety) might be adapted foruse in the present invention. Probe systems used to detect singlenucleotide polymorphisms (SNPs) might also be utilized in the presentinvention. Additional detection systems include “molecular switches,” asdisclosed in U.S. Publ. No. 20050042638, herein incorporated byreference in its entirety. Other probes, such as those comprisingintercalating dyes and/or fluorochromes, are also useful for detectionof amplification products in the present invention. See, e.g., U.S. Pat.No. 5,814,447 (herein incorporated by reference in its entirety).

ii. Data Analysis

In some embodiments, a computer-based analysis program is used totranslate the raw data generated by the detection assay (e.g., thepresence, absence, or amount of a given marker or markers) into data ofpredictive value for a clinician. The clinician can access thepredictive data using any suitable means. Thus, in some preferredembodiments, the present invention provides the further benefit that theclinician, who is not likely to be trained in genetics or molecularbiology, need not understand the raw data. The data is presenteddirectly to the clinician in its most useful form. The clinician is thenable to immediately utilize the information in order to optimize thecare of the subject.

The present invention contemplates any method capable of receiving,processing, and transmitting the information to and from laboratoriesconducting the assays, information provides, medical personal, andsubjects. For example, in some embodiments of the present invention, asample (e.g., a biopsy or a serum or urine sample) is obtained from asubject and submitted to a profiling service (e.g., clinical lab at amedical facility, genomic profiling business, etc.), located in any partof the world (e.g., in a country different than the country where thesubject resides or where the information is ultimately used) to generateraw data. Where the sample comprises a tissue or other biologicalsample, the subject may visit a medical center to have the sampleobtained and sent to the profiling center, or subjects may collect thesample themselves (e.g., a urine sample) and directly send it to aprofiling center. Where the sample comprises previously determinedbiological information, the information may be directly sent to theprofiling service by the subject (e.g., an information card containingthe information may be scanned by a computer and the data transmitted toa computer of the profiling center using an electronic communicationsystems). Once received by the profiling service, the sample isprocessed and a profile is produced (i.e., expression data), specificfor the diagnostic or prognostic information desired for the subject.

The profile data is then prepared in a format suitable forinterpretation by a treating clinician. For example, rather thanproviding raw expression data, the prepared format may represent adiagnosis or risk assessment (e.g., presence or absence of a ncRNA) forthe subject, along with recommendations for particular treatmentoptions. The data may be displayed to the clinician by any suitablemethod. For example, in some embodiments, the profiling servicegenerates a report that can be printed for the clinician (e.g., at thepoint of care) or displayed to the clinician on a computer monitor.

In some embodiments, the information is first analyzed at the point ofcare or at a regional facility. The raw data is then sent to a centralprocessing facility for further analysis and/or to convert the raw datato information useful for a clinician or patient. The central processingfacility provides the advantage of privacy (all data is stored in acentral facility with uniform security protocols), speed, and uniformityof data analysis. The central processing facility can then control thefate of the data following treatment of the subject. For example, usingan electronic communication system, the central facility can providedata to the clinician, the subject, or researchers.

In some embodiments, the subject is able to directly access the datausing the electronic communication system. The subject may chose furtherintervention or counseling based on the results. In some embodiments,the data is used for research use. For example, the data may be used tofurther optimize the inclusion or elimination of markers as usefulindicators of a particular condition or stage of disease or as acompanion diagnostic to determine a treatment course of action.

iiii. In Vivo Imaging

ncRNAs may also be detected using in vivo imaging techniques, includingbut not limited to: radionuclide imaging; positron emission tomography(PET); computerized axial tomography, X-ray or magnetic resonanceimaging method, fluorescence detection, and chemiluminescent detection.In some embodiments, in vivo imaging techniques are used to visualizethe presence of or expression of cancer markers in an animal (e.g., ahuman or non-human mammal). For example, in some embodiments, cancermarker mRNA or protein is labeled using a labeled antibody specific forthe cancer marker. A specifically bound and labeled antibody can bedetected in an individual using an in vivo imaging method, including,but not limited to, radionuclide imaging, positron emission tomography,computerized axial tomography, X-ray or magnetic resonance imagingmethod, fluorescence detection, and chemiluminescent detection. Methodsfor generating antibodies to the cancer markers of the present inventionare described below.

The in vivo imaging methods of embodiments of the present invention areuseful in the identification of cancers that express ncRNAs (e.g.,prostate cancer). In vivo imaging is used to visualize the presence orlevel of expression of a ncRNA. Such techniques allow for diagnosiswithout the use of an unpleasant biopsy. The in vivo imaging methods ofembodiments of the present invention can further be used to detectmetastatic cancers in other parts of the body.

In some embodiments, reagents (e.g., antibodies) specific for the cancermarkers of the present invention are fluorescently labeled. The labeledantibodies are introduced into a subject (e.g., orally or parenterally).Fluorescently labeled antibodies are detected using any suitable method(e.g., using the apparatus described in U.S. Pat. No. 6,198,107, hereinincorporated by reference).

In other embodiments, antibodies are radioactively labeled. The use ofantibodies for in vivo diagnosis is well known in the art. Sumerdon etal., (Nucl. Med. Biol 17:247-254 [1990] have described an optimizedantibody-chelator for the radioimmunoscintographic imaging of tumorsusing Indium-111 as the label. Griffin et al., (J Clin Onc 9:631-640[1991]) have described the use of this agent in detecting tumors inpatients suspected of having recurrent colorectal cancer. The use ofsimilar agents with paramagnetic ions as labels for magnetic resonanceimaging is known in the art (Lauffer, Magnetic Resonance in Medicine22:339-342 [1991]). The label used will depend on the imaging modalitychosen. Radioactive labels such as Indium-111, Technetium-99m, orIodine-131 can be used for planar scans or single photon emissioncomputed tomography (SPECT). Positron emitting labels such asFluorine-19 can also be used for positron emission tomography (PET). ForMRI, paramagnetic ions such as Gadolinium (III) or Manganese (II) can beused.

Radioactive metals with half-lives ranging from 1 hour to 3.5 days areavailable for conjugation to antibodies, such as scandium-47 (3.5 days)gallium-67 (2.8 days), gallium-68 (68 minutes), technetiium-99m (6hours), and indium-111 (3.2 days), of which gallium-67, technetium-99m,and indium-111 are preferable for gamma camera imaging, gallium-68 ispreferable for positron emission tomography.

A useful method of labeling antibodies with such radiometals is by meansof a bifunctional chelating agent, such as diethylenetriaminepentaaceticacid (DTPA), as described, for example, by Khaw et al. (Science 209:295[1980]) for In-111 and Tc-99m, and by Scheinberg et al. (Science215:1511 [1982]). Other chelating agents may also be used, but the1-(p-carboxymethoxybenzyl)EDTA and the carboxycarbonic anhydride of DTPAare advantageous because their use permits conjugation without affectingthe antibody's immunoreactivity substantially.

Another method for coupling DPTA to proteins is by use of the cyclicanhydride of DTPA, as described by Hnatowich et al. (Int. J. Appl.Radiat. Isot. 33:327 [1982]) for labeling of albumin with In-111, butwhich can be adapted for labeling of antibodies. A suitable method oflabeling antibodies with Tc-99m which does not use chelation with DPTAis the pretinning method of Crockford et al., (U.S. Pat. No. 4,323,546,herein incorporated by reference).

A method of labeling immunoglobulins with Tc-99m is that described byWong et al. (Int. J. Appl. Radiat. Isot., 29:251 [1978]) for plasmaprotein, and recently applied successfully by Wong et al. (J. Nucl.Med., 23:229 [1981]) for labeling antibodies.

In the case of the radiometals conjugated to the specific antibody, itis likewise desirable to introduce as high a proportion of theradiolabel as possible into the antibody molecule without destroying itsimmunospecificity. A further improvement may be achieved by effectingradiolabeling in the presence of the ncRNA, to insure that the antigenbinding site on the antibody will be protected. The antigen is separatedafter labeling.

In still further embodiments, in vivo biophotonic imaging (Xenogen,Almeda, Calif.) is utilized for in vivo imaging. This real-time in vivoimaging utilizes luciferase. The luciferase gene is incorporated intocells, microorganisms, and animals (e.g., as a fusion protein with acancer marker of the present invention). When active, it leads to areaction that emits light. A CCD camera and software is used to capturethe image and analyze it.

iv. Compositions & Kits

Compositions for use in the diagnostic methods described herein include,but are not limited to, probes, amplification oligonucleotides, and thelike.

The probe and antibody compositions of the present invention may also beprovided in the form of an array.

II. Drug Screening Applications

In some embodiments, the present invention provides drug screeningassays (e.g., to screen for anticancer drugs). The screening methods ofthe present invention utilize ncRNAs. For example, in some embodiments,the present invention provides methods of screening for compounds thatalter (e.g., decrease) the expression or activity of ncRNAs. Thecompounds or agents may interfere with transcription, by interacting,for example, with the promoter region. The compounds or agents mayinterfere with mRNA (e.g., by RNA interference, antisense technologies,etc.). The compounds or agents may interfere with pathways that areupstream or downstream of the biological activity of ncRNAs. In someembodiments, candidate compounds are antisense or interfering RNA agents(e.g., oligonucleotides) directed against ncRNAs. In other embodiments,candidate compounds are antibodies or small molecules that specificallybind to a ncRNAs regulator or expression products inhibit its biologicalfunction.

In one screening method, candidate compounds are evaluated for theirability to alter ncRNAs expression by contacting a compound with a cellexpressing a ncRNA and then assaying for the effect of the candidatecompounds on expression. In some embodiments, the effect of candidatecompounds on expression of ncRNAs is assayed for by detecting the levelncRNA expressed by the cell. mRNA expression can be detected by anysuitable method.

EXPERIMENTAL

The following examples are provided in order to demonstrate and furtherillustrate certain preferred embodiments and aspects of the presentinvention and are not to be construed as limiting the scope thereof.

Example 1 A. Methods

Methods Summary

All prostate tissue samples were obtained from the University ofMichigan Specialized Program Of Research Excellence (S.P.O.R.E.) usingan IRB-approved informed consent protocol. Next generation sequencingand library preparation was performed as previously described (Maher etal., Proc Natl Acad Sci USA 106 (30), 12353 (2009)). Uniquely mappingsequencing reads were aligned with TopHat and sequencing data for allsamples was merged. Ab initio transcriptome assembly was performed byaligning sequences with TopHat and using uniquely mapped read positionsto build transcripts with Cufflinks. Informatics approaches were used torefine the assembly and predict expressed transcriptional units.Unannotated transcripts were nominated based upon their absence in theUCSC, RefSeq, ENSEMBL, ENCODE, and Vega databases. Differentialexpression was determined using the Significance Analysis of Microarrays(SAM) algorithm (Tusher et al., Proc Natl Acad Sci USA 98 (9), 5116(2001)) on log 2 mean expression in benign, cancer, and metastaticsamples. Cancer outlier profile analysis (COPA) was performed aspreviously described (Tomlins et al., Science 310 (5748), 644 (2005))with slight modifications. PCR experiments were performed according tostandard protocols, and RACE was performed with the GeneRacer Kit(Invitrogen) according to manufacturer's instructions. ChIP-seq data wasobtained from previously published data (Yu et al., Cancer Cell 17 (5),443). siRNA knockdown was performed with custom siRNA oligos (Dharmacon)with Oligofectamine (Invitrogen). Transmembrane invasion assays wereperformed with Matrigel (BD Biosciences) and cell proliferation assayswere performed by cell count with a Coulter counter. Urine analyses wereperformed as previously described (Laxman et al., Cancer Res 68 (3), 645(2008)) with minor modifications.

Cell Lines and Tissues

The benign immortalized prostate cell line RWPE as well as PC3, Du145,LNCaP, VCaP, 22Rv1, CWR22, C4-2B, NCI-660, MDA PCa 2b, WPMY-1, andLAPC-4 prostate cell lines were obtained from the American Type CultureCollection (Manassas, Va.). Benign non-immortalized prostate epithelialcells (PrEC) and prostate smooth muscle cells (PrSMC) were obtained fromLonza (Basel, Switzerland). Cell lines were maintained using standardmedia and conditions. For androgen treatment experiments, LNCaP and VCaPcells were grown in androgen depleted media lacking phenol red andsupplemented with 10% charcoal-stripped serum and 1%penicillin-streptomycin. After 48 hours, cells were treated with 5 nMmethyltrienolone (R1881, NEN Life Science Products) or an equivalentvolume of ethanol. Cells were harvested for RNA at 6, 24, and 48 hourspost-treatment. Prostate tissues were obtained from the radicalprostatectomy series and Rapid Autopsy Program at the University ofMichigan tissue core. These programs are part of the University ofMichigan Prostate Cancer Specialized Program Of Research Excellence(S.P.O.R.E.). All tissue samples were collected with informed consentunder an Institutional Review Board (IRB) approved protocol at theUniversity of Michigan.

PC3, Du145, LNCaP, 22Rv1, and CRW22 cells were grown in RPMI 1640(Invitrogen) and supplemented with 10% fetal bovine serum (FBS) and 1%penicillin-streptomycin. LNCaP CDS parent cells were grown in RPMI 1640lacking phenol red (Invitrogen) supplemented with 10% charcoal-dextranstripped FBS (Invitrogen) and 1% penicillin-streptomycin. LNCaP CDS 1,2, and 3 are androgen-independent subclones derived from extended cellculture in androgendepleted media. VCaP and WPMY-1 cells were grown inDMEM (Invitrogen) and supplemented with 10% fetal bovine serum (FBS)with 1% penicillin-streptomycin. NCI-H660 cells were grown in RPMI 1640supplemented with 0.005 mg/ml insulin, 0.01 mg/ml transferring, 30 nMsodium selenite, 10 nM hydrocortisone, 10 nM beta-estradiol, 5% FBS andan extra 2 mM of L-glutamine (for a final concentration of 4 mM). MDAPCa 2b cells were grown in F-12K medium (Invitrogen) supplemented with20% FBS, 25 ng/ml cholera toxin, 10 ng/ml EGF, 0.005 mMphosphoethanolamine, 100 pg/ml hydrocortisone, 45 nM selenious acid, and0.005 mg/ml insulin. LAPC-4 cells were grown in Iscove's media(Invitrogen) supplemented with 10% FBS and 1 nM R1881. C4-2B cells weregrown in 80% DMEM supplemented with 20% F12, 5% FBS, 3 g/L NaCo₃, 5μg/ml insulin, 13.6 pg/ml triiodothyonine, 5 μg/ml transferrin, 0.25μg/ml biotin, and 25 μg/ml adenine. PrEC cells were grown in PrEGMsupplemented with 2 ml BPE, 0.5 ml hydrocortisone, 0.5 ml EGF, 0.5 mlepinephrine, 0.5 ml transferring, 0.5 ml insulin, 0.5 ml retinoic acid,and 0.5 ml triiodothyronine, as part of the PrEGM BulletKit (Lonza).PrSMC cells were grown in SmGM-2 media supplemented with 2 ml BPE, 0.5ml hydrocortisone, 0.5 ml EGF, 0.5 ml epinephrine, 0.5 ml transferring,0.5 ml insulin, 0.5 ml retinoic acid, and 0.5 ml triiodothyronine, aspart of the SmGM-2 BulletKit (Lonza).

RNA-Seq Library Preparation.

Next generation sequencing of RNA was performed on 21 prostate celllines, 20 benign adjacent prostates, 47 localized tumors, and 14metastatic tumors according to Illumina's protocol using 2 μg of RNA.RNA integrity was measured using an Agilent 2100 Bioanalyzer, and onlysamples with a RIN score >7.0 were advanced for library generation. RNAwas poly-A+ selected using the OligodT beads provided by Ilumina andfragmented with the Ambion Fragmentation Reagents kit (Ambion, Austin,Tex.). cDNA synthesis, end-repair, A-base addition, and ligation of theIllumina PCR adaptors (single read or paired-end where appropriate) wereperformed according to Illumina's protocol. Libraries were thensize-selected for 250-300 bp cDNA fragments on a 3.5% agarose gel andPCR-amplified using Phusion DNA polymerase (Finnzymes) for 15-18 PCRcycles. PCR products were then purified on a 2% agarose gel andgel-extracted. Library quality was credentialed by assaying each libraryon an Agilent 2100 Bioanalyzer of product size and concentration.Libraries were sequenced as 36-45mers on an Illumina Genome Analyzer Ior Genome Analyzer II flowcell according to Illumina's protocol. Allsingle read samples were sequenced on a Genome Analyzer I, and allpaired-end samples were sequenced on a Genome Analyzer II.

RNA Isolation and cDNA Synthesis

Total RNA was isolated using Trizol and an RNeasy Kit (Invitrogen) withDNase I digestion according to the manufacturer's instructions. RNAintegrity was verified on an Agilent Bioanalyzer 2100 (AgilentTechnologies, Palo Alto, Calif.). cDNA was synthesized from total RNAusing Superscript III (Invitrogen) and random primers (Invitrogen).

Quantitative Real-Time PCR

Quantitative Real-time PCR (qPCR) was performed using Power SYBR GreenMastermix (Applied Biosystems, Foster City, Calif.) on an AppliedBiosystems 7900HT Real-Time PCR System. All oligonucleotide primers wereobtained from Integrated DNA Technologies (Coralville, Iowa) and arelisted in Table 13. The housekeeping gene, GAPDH, was used as a loadingcontrol. Fold changes were calculated relative to GAPDH and normalizedto the median value of the benign samples.

Reverse-Transcription PCR

Reverse-transcription PCR (RT-PCR) was performed for primer pairs usingPlatinum Taq High Fidelity polymerase (Invitrogen). PCR products wereresolved on a 2% agarose gel. PCR products were either sequenceddirectly (if only a single product was observed) or appropriate gelproducts were extracted using a Gel Extraction kit (Qiagen) and clonedinto pcr4-TOPO vectors (Invitrogen). PCR products were bidirectionallysequenced at the University of Michigan Sequencing Core using eithergene-specific primers or M13 forward and reverse primers for cloned PCRproducts. All oligonucleotide primers were obtained from Integrated DNATechnologies (Coralville, Iowa) and are listed in Table 13.

RNA-Ligase-Mediated Rapid Amplification of cDNA Ends (RACE)

5′ and 3′ RACE was performed using the GeneRacer RLM-RACE kit(Invitrogen) according to the manufacturer's instructions. RACE PCRproducts were obtained using Platinum Taq High Fidelity polymerase(Invitrogen), the supplied GeneRacer primers, and appropriategene-specific primers indicated in Table 13. RACEPCR products wereseparated on a 2% agarose gels. Gel products were extracted with a GelExtraction kit (Qiagen), cloned into pcr4-TOPO vectors (Invitrogen), andsequenced bidirectionally using M13 forward and reverse primers at theUniversity of Michigan Sequencing Core. At least three colonies weresequenced for every gel product that was purified.

Paired-End Next-Generation Sequencing of RNA

2 μg total RNA was selected for polyA+RNA using Sera-Mag oligo(dT) beads(Thermo Scientific), and paired-end next-generation sequencing librarieswere prepared as previously described (Maher et al., supra) usingIllumina-supplied universal adaptor oligos and PCR primers (Illumina).Samples were sequenced in a single lane on an Illumina Genome AnalyzerII flowcell using previously described protocols (Maher et al., supra).36-45 mer paired-end reads were according to the protocol provided byIllumina.

siRNA Knockdown Studies

Cells were plated in 100 mM plates at a desired concentration andtransfected with 20 μM experimental siRNA oligos or non-targetingcontrols twice, at 12 hours and 36 hours post-plating. Knockdowns wereperformed with Oligofectamine and Optimem. Knockdown efficiency wasdetermined by qPCR. 72 hours post-transfection, cells were trypsinized,counted with a Coulter counter, and diluted to 1 million cells/mL. Forproliferation assays, 200,000 cells were plated in 24-well plates andgrown in regular media. 48 and 96 hours post-plating, cells wereharvested and counted using a Coulter counter. For invasion assays,Matrigel was diluted 1:4 in serum-free media and 100 μL of the dilutedMatrigel was applied to a Boyden chamber transmembrane insert andallowed to settle overnight at 37° C. 200,000 cells suspended inserum-free media were applied per insert and 500 μL of serum-containingmedia was placed in the bottom of the Boyden (fetal bovine serumfunctioning as a chemoattractant). Cells were allowed to invade for 48hours, at which time inserts were removed and noninvading cells andMatrigel were gently removed with a cotton swab. Invading cells werestained with crystal violet for 15 minutes and air-dried. Forcolorimetric assays, the inserts were treated with 200 μl of 10% aceticacid and the absorbance at 560 nm was measured using aspectrophotometer. For WST-1 assays, 20,000 cells were plated into96-well plates and grown in 100 μL of serum-containing media. 48 and 96hours post-plating, cells were measured for viability by adding 10 μL ofWST-1 reagent to the cell media, incubating for 2 hours at 37° C. andmeasuring the absorbance at 450 nM using a spectrophotomer.

Urine qPCR

Urine samples were collected from 120 patients with informed consentfollowing a digital rectal exam before either needle biopsy or radicalprostatectomy at the University of Michigan with Institutional ReviewBoard approval as described previously (Laxman et al., Cancer Res 68(3), 645 (2008)). Isolation of RNA from urine and TransPlex wholetranscriptome amplification were performed as described previously(Laxman et al., Neoplasia 8 (10), 885 (2006)). qPCR on urine samples wasperformed for KLK3 (PSA), TMPRSS2-ERG, GAPDH, PCA3, PCAT-1 and PCAT-14using Power SYBR Mastermix (Applied Biosystems) as described above. RawCt values were extracted and normalized in the following manner. First,samples with GAPDH Ct values >25 or KLK3 Ct values >30 were removed fromanalysis to ensure sufficient prostate cell collection, leaving 10⁸samples for analysis. The GAPDH and KLK3 raw Ct values were average foreach sample. ΔCt analysis was performed by measuring each value againstthe average of CtGAPDH and CtKLK3, and ΔCt values were normalized to themedian ΔCt of the benign samples. Fold change was then calculated at2-ΔCt. Samples were considered to be prostate cancer ifhistopathological analysis observed cancer or if the TMPRSS2-ERGtranscript achieved a Ct value <37. Benign samples were defined assamples with normal histology and TMPRSS2-ERG transcript Ct values >37.

Statistical Analyses for Experimental Studies

All data are presented as means±s.e.m. All experimental assays wereperformed in duplicate or triplicate.

Bioinformatics Analyses

To achieve an ab initio prediction of the prostate cancer transcriptomeexisting publicly tools for mapping, assembly, and quantification oftranscripts were supplemented with additional informatics filteringsteps to enrich the results for the most robust transcript predictions(FIG. 6a ). Transcripts were then identified and classified by comparingthem against gene annotation databases (FIG. 6b ). Details of thebioinformatics analyses are provided below.

Mapping Reads with TopHat

Reads were aligned using TopHat v1.0.13 (Feb. 5, 2010) (Trapnell et al.,Bioinformatics 25, 1105-11 (2009)), a gapped aligner capable ofdiscovering splice junctions ab initio. Briefly, TopHat aligns reads tothe human genome using Bowtie (Langmead et al., Genome Biol 10, R25(2009)) to determine a set of “coverage islands” that may representputative exons. TopHat uses these exons as well as the presence of GT-AGgenomic splicing motifs to build a second set of reference sequencesspanning exon-exon junctions. The unmapped reads from the initial genomealignment step are then remapped against this splice junction referenceto discover all the junction-spanning reads in the sample. TopHatoutputs the reads that successfully map to either the genome or thesplice junction reference in SAM format for further analysis. For thisstudy a maximum intron size of 500 kb, corresponding to over 99.98% ofRefSeq (Wheeler et al. Nucleic Acids Res 28, 10-4 (2000)) introns wasused. For sequencing libraries the insert size was determined using anAgilent 2100 Bioanalyzer prior to data analysis, and it was found thatthis insert size agreed closely with software predictions. An insertsize standard deviation of 20 bases was chosen in order to match themost common band size cut from gels during library preparation. Intotal, 1.723 billion fragments were generated from 201 lanes ofsequencing on the Illumina Genome Analyzer and Illumina Genome AnalyzerII. Reads were mapped to the human genome (hg18) downloaded from theUCSC genome browser website (Karolchik et al., Nucleic Acids Res 31,51-4 (2003); Kent et al., Genome Res 12, 996-1006 (2002)). 1.418 billionunique alignments were obtained, including 114.4 million splicejunctions for use in transcriptome assembly. Reads with multiplealignments with less than two mismatches were discarded.

Ab Initio Assembly and Quantification with Cufflinks

Aligned reads from TopHat were assembled into sample-specifictranscriptomes with Cufflinks version 0.8.2 (Mar. 26, 2010) (Trapnell etal., Nat Biotechnol 28, 511-5). Cufflinks assembles exonic andsplice-junction reads into transcripts using their alignmentcoordinates. To limit false positive assemblies a maximum introniclength of 300 kb, corresponding to the 99.93% percentile of knownintrons was used. After assembling transcripts, Cufflinks computesisoform-level abundances by finding a parsimonious allocation of readsto the transcripts within a locus. Transcripts with abundance less than15% of the major transcript in the locus, and minor isoforms withabundance less than 5% of the major isoform were filtered. Defaultsettings were used for the remaining parameters.

The Cufflinks assembly stage yielded a set of transcript annotations foreach of the sequenced libraries. The transcripts were partitioned bychromosome and the Cuffcompare utility provided by Cufflinks was used tomerge the transcripts into a combined set of annotations. TheCuffcompare program performs a union of all transcripts by mergingtranscripts that share all introns and exons. The 5′ and 3′ exons oftranscripts were allowed to vary by up to 100 nt during the comparisonprocess.

Distinguishing Transcripts from Background Signal

Cuffcompare reported a total of 8.25 million distinct transcripts.Manual inspection of these transcripts in known protein coding generegions indicated that most of the transcripts were likely to be poorquality reconstructions of overlapping larger transcripts. Also, many ofthe transcripts were unspliced and had a total length smaller than thesize selected fragment length of approximately ˜250 nt. Furthermore,many of these transcripts were only present in a single sample. Astatistical classifier to predict transcripts over background signal wasdesigned to identify highly recurrent transcripts that may be altered inprostate cancer. AceView (Thierry-Mieg et al. Genome Biol 7 Suppl 1, S121-14 (2006)) were used. For each transcript predicted by Cufflinks thefollowing statistics were collected: length (bp), number of exons,recurrence (number of samples in which the transcript was predicted),95th percentile of abundance (measured in Fragments per Kilobase perMillion reads (FPKM)) across all samples, and uniqueness of genomic DNAharboring the transcript transcript (measured using the Rosettauniqueness track from UCSC (Rhead et al. 2010. Nucleic Acids Res 38,D613-9). Using this information, recursive partitioning and regressiontrees in R (package rpart) were used to predict, for each transcript,whether its expression patterns and structural properties resembledthose of annotated genes. Classification was performed independently foreach chromosome in order to incorporate the effect of gene densityvariability on expression thresholds. Transcripts that were notclassified as annotated genes were discarded, and the remainder weresubjected to additional analysis and filtering steps. By examining thedecision tree results it was observed that the 95th percentile ofexpression across all samples as well as the recurrence of eachtranscript were most frequently the best predictors of expressed versusbackground transcripts (FIG. 7).

Refinement of Transcript Fragments

The statistical classifier predicted a total 2.88 million (34.9%)transcript fragments as “expressed” transcripts. A program was developedto extend and merge intron-redundant transcripts to produce a minimumset of transcripts that describes the assemblies produced by Cufflinks.The merging step produced a total of 123,554 independent transcripts.Tanscript abundance levels were re-computed for these revisedtranscripts in Reads per Kilobase per Million (RPKM) units. Theseexpression levels were used for the remainder of the study. Severaladditional filtering steps were used to isolate the most robusttranscripts. First, transcripts with a total length less than 200 ntwere discarded. Single exon transcripts with greater than 75% overlap toanother longer transcript were also discarded. Transcripts that lacked acompletely unambiguous genomic DNA stretch of at least 40 nt were alsoremoved. Genomic uniqueness was measured using the Rosetta uniquenesstrack downloaded from the UCSC genome browser website. Transcripts thatwere not present in at least 5% of the cohort (>5 samples) at more than5.0 RPKM were retained.

In certain instances transcripts were observed that were interrupted bypoorly mappable genomic regions. Additionally, for low abundance genesfragmentation due to the lack of splice junction or paired-end readevidence needed to connect nearby fragments were observed. Thedifference in the Pearson correlation between expression of randomlychosen exons on the same transcript versus expression of spatiallyproximal exons on different transcripts was measured and it was foundthat in the cohort, a Pearson correlation >0.8 had a positive predictivevalue (PPV) of >95% for distinct exons to be part of the sametranscript. Using this criteria, hierarchical agglomerative clusteringto extend transcript fragments into larger transcriptional units wasperformed. Pairs of transcripts further than 100 kb apart, transcriptson opposite strands, and overlapping transcripts were not considered forclustering. Groups of correlated transcripts were merged, and introns<40 nt in length were removed.

Comparison with Gene Annotation Databases

The 44,534 transcripts produced by the bioinformatics pipeline wereclassified by comparison with a comprehensive list of “annotated”transcripts from UCSC, RefSeq, ENCODE, Vega, and Ensembl. First,transcripts corresponding to processed pseudogenes were separated. Thiswas done to circumvent a known source of bias in the TopHat readaligner. TopHat maps reads to genomic DNA in its first step,predisposing exon-exon junction reads to align to their splicedretroposed pseudogene homologues. Next, transcripts with >1 bp ofoverlap with at least one annotated gene on the correct strand weredesignated “annotated”, and the remainder were deemed “unannotated”.Transcripts with no overlap with protein coding genes were subdividedinto intronic, intergenic, or partially intronic antisense categoriesbased on their relative genomic locations.

Informatics Filtering of Unspliced Pre-mRNA Isoforms

An increase in the percentage of intronic transcripts in the assemblyrelative to known intronic ncRNAs was observed. This led to theobservation that in many cases unspliced pre mRNAs appear at sufficientlevels to escape the filtering steps employed by Cufflinks during theassembly stage. Intronic and antisense transcripts that were correlated(Pearson correlation >0.5) to their overlapping protein coding geneswere removed. This effectively removed transcripts within genes such asPCA3 and HPN that were obvious premRNA artifacts, while leaving trulynovel intronic transcripts—such as those within FBXL7 and CDH13—intact.These steps produced a consensus set of 35,415 transcripts supportinglong polyadenylated RNA molecules in human prostate tissues and celllines. Per chromosome transcript counts closely mirrored knowntranscript databases (Table 2), indicating that the informaticsprocedures employed compensate well for gene density variability acrosschromosomes. Overall a similar number of transcripts as present in theeither the RefSeq or UCSC databases (Wheeler et al. Nucleic Acids Res28, 10-4 (2000)) were detected.

Coding Potential Analysis

To analyze coding potential, DNA sequences for each transcript wereextracted and searched for open reading frames (ORFs) using thetxCdsPredict program from the UCSC source tool set (Kent et al. GenomeRes 12, 996-1006 (2002)). This program produces a score corresponding tothe protein coding capacity of a given sequence, and scores >800 are˜90% predictive of protein coding genes. This threshold was used tocount transcripts with coding potential, and found only 5 of 6,641unannotated genes with scores >800, compared with 1,669 of 25,414protein coding transcripts. Additionally, it was observed that proteincoding genes possess consistently longer ORFs than either unannotated orannotated ncRNA transcripts, indicating that the vast majority of theunannotated transcripts represent ncRNAs (FIG. 10).

Separation of Transcripts into Repetitive and Non-Repetitive Categories

To separate transcripts into “repeat” and “non-repeat” transcripts, thegenomic DNA corresponding to the transcript exons was extracted and thefraction of repeat-masked nucleotides in each sequence were calculated.For the designation of repeat classes, RepMask 3.2.7 UCSC Genome Browsertrack (Kent, supra) was used. It was observed that transcripts enrichedwith repetitive DNA tended to be poorly conserved and lacked ChIP-seqmarks of active chromatin (FIG. 12). Transcripts containing >25%repetitive DNA (FIG. 11) were separated for the purposes of the ChIP-seqand conservation analyses discussed below.

Conservation Analysis

The SiPhy package (Garber et al. Bioinformatics 25, i54-62 (2009)) wasused to estimate the locate rate of variation (w) of all non-repetitivetranscript exons across 29 placental mammals. The program was run asdescribed on the SiPhy website.

ChIP-Seq Datasets

Published ChIP-Seq datasets for H3K4me1, H3K4me2, H3K4me3, AcetylatedH3, Pan-H3, and H3K36me3 were used (Yu et al. Cancer Cell 17, 443-54).These data are publically available through the NCBI Geo Omnibus (GEOGSM353632). The raw ChIP-Seq data was analyzed using MACS34 (H3K4me1,H3K4me2, H3K4me3, Acetylated H3, and Pan-H3) or SICER35 (H3K36me3) peakfinder programs using default settings. These peak finders were usedbased upon their preferential suitability to detect different types ofhistone modifications (Pepke et al., Nat Methods 6, S22-32 (2009)). TheH3K4me3-H3K36me3 chromatin signature used to identify lincRNAs wasdetermined from the peak coordinates by associating each H3K4me3 peakwith the closest H3K36me3-enriched region up to a maximum of 10 kb away.The enhancer signature (H3K4me1 but not H3K4me3) was determined bysubtracting the set of overlapping H3K4me3 peaks from the entire set ofH3K4me1 peaks. These analyses were performed with the bx-pythonlibraries distributed as part of the Galaxy bioinformaticsinfrastructure.

Differential Expression Analysis

To predict differentially expressed transcripts a matrix oflog-transformed, normalized RPKM expression values was prepared by usingthe base 2 logarithm after adding 0.1 to all RPKM values. The data werefirst centered by subtracting the median expression of the benignsamples for each transcript. The Significance Analysis of Microarrays(SAM) method (Tusher et al., Proc Natl Acad Sci USA 98, 5116-21 (2001))with 250 permutations of the Tusher et al. S0 selection method was usedto predict differentially expressed genes. A delta value correspondingto the 90th percentile FDR desired for individual analyses was used. TheMultiExperiment Viewer application (Chu et al., Genome Biol 9, R118(2008)) was used to run SAM and generate heatmaps. It was confirmed thatthe results matched expected results through comparison with microarraysand known prostate cancer biomarkers.

Outlier Analysis

A modified COPA analysis was performed on the 81 tissue samples in thecohort. RPKM expression values were used and shifted by 1.0 in order toavoid division by zero. The COPA analysis had the following steps(MacDonald & Ghosh, Bioinformatics 22, 2950-1 (2006); Tomlins et al.Science 310, 644-8 (2005)): 1) gene expression values were mediancentered, using the median expression value for the gene across the allsamples in the cohort. This sets the gene's median to zero. 2) Themedian absolute deviation (MAD) was calculated for each gene, and theneach gene expression value was scaled by its MAD. 3) The 80, 85, 90, 98percentiles of the transformed expression values were calculated foreach gene and the average of those four values was taken. Then, geneswere rank ordered according to this “average percentile”, whichgenerated a list of outliers genes arranged by importance. 4) Finally,genes showing an outlier profile in the benign samples were discarded.Six novel transcripts ranked as both outliers anddifferentially-expressed genes in the analyses. These six were manuallyclassified either as differentially-expressed or outlier status based onwhat each individual's distribution across samples indicated.

Repeat Enrichment Analysis

To assess the enrichment of repetitive elements in the assembly, 100random permutations of the transcript positions on the same chromosomeand strand were generated. To mirror the original constraints used tonominate transcripts it was ensured that permuted transcript positionscontained a uniquely mappable stretch of genomic DNA at least 50 ntlong. To account for the effects of mappability difficulties, each exonwas padded by ±0 bp, 50 bp, 100 bp, or 500 bp of additional genomicsequence before intersecting the exons with repeat elements in theRepeatMasker 3.2.7 database. It was observed that padding by more than50 bp did not improve enrichment results and padded exons by ±50 bp insubsequent analyses and tests (Table 9). Finally, the Shapiro-Wilk testfor normality was performed and it was verified that the number ofmatches to highly abundant repetitive element types was approximatelynormally distributed.

B. Results

Prostate Cancer Transcriptome Sequencing

Transcriptome sequencing (RNA-Seq) was performed on 21 prostate celllines, 20 benign adjacent prostates (benign), 47 localized tumors (PCA),and 14 metastatic tumors (MET). A total of 201 RNA-Seq libraries fromthis cohort were sequenced yielding a total of 1.41 billion mappedreads, with a median 4.70 million mapped reads per sample (Table 1 forsample information).

To analyze these data a method for ab initio transcriptome assembly toreconstruct transcripts and transcript abundance levels was used (FIG. 6and Table 2) (Trapnell et al., Nat Biotechnol 28 (5), 511; Trapnell etal., Bioinformatics 25 (9), 1105 (2009)). Sample-specific transcriptomeswere predicted and individual predication were merged into a consensustranscriptome and the most robust transcripts were retained (FIG. 7).The ab initio transcriptome assembly and subsequent refinement stepsyielded 35,415 distinct transcriptional loci (see FIG. 8 for examples).

The assembled transcriptome was compared to the UCSC, Ensembl, Refseq,Vega, and ENCODE gene databases to identify and categorize transcripts.While the majority of the transcripts (77.3%) corresponded to annotatedprotein coding genes (72.1%) and noncoding RNAs (5.2%), a significantpercentage (19.8%) lacked any overlap and were designated “unannotated”(FIG. 1a ). These included partially intronic antisense (2.44%), totallyintronic (12.1%), and intergenic transcripts (5.25%). These resultsagree with previous data indicating that large fractions of thetranscriptome represent unannotated transcription (Birney et al., Nature447 (7146), 799 (2007); Carninci et al., Science 309 (5740), 1559 (2005)and that significant percentages of genes may harbor related antisensetranscripts (He et al., Science 322 (5909), 1855 (2008); Yelin et al.,Nat Biotechnol 21 (4), 379 (2003)). Due to the added complexity ofcharacterizing antisense or partially intronic transcripts withoutstrand-specific RNA-Seq libraries, studies focused on totally intronicand intergenic transcripts.

Characterization of Novel Transcripts

Global characterization of novel transcripts corroborated previousreports that they are relatively poorly conserved and more lowlyexpressed than protein coding genes (Guttman et al., Nat Biotechnol 28(5), 503; Guttman et al., Nature 458 (7235), 223 (2009)). Expressionlevels of unannotated prostate cancer transcripts were consistentlyhigher than randomly permuted controls, but lower than annotated ncRNAsor protein coding genes (FIG. 1b ). Unannotated transcripts also showedless overlap with known expressed sequence tags (ESTs) thanprotein-coding genes but more than randomly permuted controls (FIG. 5).Unannotated transcripts showed a clear but subtle increase inconservation over control genomic intervals (novel intergenictranscripts p=2.7×10-4±0.0002 for 0.4<ω<0.8; novel intronic transcriptsp=2.6×10-5±0.0017 for 0<ω<0.4, FIG. 1c ). Only a small subset of novelintronic transcripts showed increased conservation (FIG. 1c insert), butthis conservation was quite profound. By contrast, a larger number ofnovel intergenic transcripts showed more mild increases in conservation.Finally, analysis of coding potential revealed that only 5 of 6,144transcripts harbored a high quality open reading frame (ORF), indicatingthat the overwhelming majority of these transcripts represent ncRNAs(FIG. 10).

Next, published prostate cancer ChIP-Seq data for two prostate celllines (Yu et al., Cancer Cell 17 (5), 443; VCaP and LNCaP was used inorder to interrogate the overlap of unannotated transcripts with histonemodifications supporting active transcription (H3K4me1, H3K4me2,H3K4me3, H3K36me3, Acetyl-H3 and RNA polymerase II, see Table 3).Because unannotated ncRNAs showed two clear subtypes, repeat-associatedand non-repeats (FIG. 11 and discussed below), it was contemplated thatthese two subtypes may display distinct histone modifications as notedin previous research (Day et al., Genome Biol 11 (6), R69). Whereasnon-repeat transcripts showed strong enrichment for hi stone marks ofactive transcription at their putative transcriptional start sites(TSSs), repeat-associated transcripts showed virtually no enrichment(FIG. 12), and for the remaining ChIP-Seq analyses non-repeattranscripts only were considered. In this set of unannotatedtranscripts, strong enrichment for histone modifications characterizingTSSs and active transcription, including H3K4me2, H3K4me3, Acetyl-H3 andRNA Polymerase II (FIG. 1d-g ) but not H3K4me1 was observed, whichcharacterizes enhancer regions (FIGS. 13 and 14). Intergenic ncRNAsperformed much better in these analyses than intronic ncRNAs (FIG. 1d-g). To elucidate global changes in transcript abundance between prostatecancer and benign tissues, differential expression was performedanalysis for all transcripts. 836 genes differentially-expressed betweenbenign and PCA samples (FDR<0.01) were found, with protein-coding genesconstituting 82.8% of all differentially-expressed genes (FIG. 1h andTable 4). This category contained the most significant transcripts,including numerous known prostate cancer genes such as AMACR32 andHepsin (Dhanasekaran et al., Nature 412 (6849), 822 (2001)). AnnotatedncRNAs represented 7.4% of differentially-expressed genes, including thencRNA PCA334, which resides within an intron of the PRUNE2 gene andranked #4 overall (12.2 fold change; adj. p<2×10-4, Wilcoxon rank sumtest, Benjamini-Hochberg correction) (FIG. 8). Finally, 9.8% ofdifferentially-expressed genes corresponded to unannotated ncRNAs,including 3.2% within gene introns and 6.6% in intergenic regions,indicating that these species contribute significantly to the complexityof the prostate cancer transcriptome.

Dysregulation of Unannotated Non-Coding RNAs

Recent reports of functional long intervening non-coding RNAs(Dhanasekaran et al., Nature 412 (6849), 822 (2001); Gupta et al.,Nature 464 (7291), 1071; Rinn et al., Cell 129 (7), 1311 (2007); Guttmanet al., Nature 458 (7235), 223 (2009)) (lincRNAs) in intergenic regionsled to an exploration of intergenic ncRNAs further. A total of 1859unannotated intergenic RNAs were found throughout the human genome. Thepresent invention is not limited to a particular mechanism. Indeed, anunderstanding of the mechanism is not necessary to practice the presentinvention. Nonetheless it is contemplated that this is an underestimatedue to the inability to detect small RNAs eliminated by the ˜250 bp sizeselection performed during RNA-Seq library generation (Methods).Overall, novel intergenic RNAs resided closer to protein-coding genesthan protein-coding genes do to each other (the median distance to thenearest protein-coding gene is 4292 kb for novel genes and 8559 kb forprotein-coding genes, FIG. 2a ). For instance, if two protein-codinggenes, Gene A and Gene B, are separated by the distance AB, then thefurthest an unannotated ncRNA can be from both of them is 0.5*AB, whichis exactly what was observed (4292/8559=0.501). Supporting thisobservation, 34.1% of unannotated transcripts are located ≧10 kb fromthe nearest protein-coding gene. As an example, the Chr15q arm wasvisualized using the Circos program. Eighty-nine novel intergenictranscripts were nominated across this chromosomal region, includingseveral differentially-expressed loci centromeric to TLE3 (FIG. 2b )which were validated by PCR in prostate cancer cell lines (FIG. 15). Afocused analysis of the 1859 novel intergenic RNAs yielded 106 that weredifferentially expressed in localized tumors (FDR<0.05; FIG. 2c ). TheseProstate Cancer Associated Transcripts (PCATs) were ranked according totheir fold change in localized tumor versus benign tissue (Tables 5 and6).

Similarly, performing a modified cancer outlier profile analysis (COPA)on the RNA-Seq dataset re-discovered numerous known prostate canceroutliers, such as ERG7, ETV17, SPINK135, and CRISP336,37, and nominatednumerous unannotated ncRNAs as outliers (FIG. 2d and Tables 6 and 7).Merging the results from the differential expression and COPA analysesresulted in a set of 121 unannotated transcripts that accuratelydiscriminated benign, localized tumor, and metastatic prostate samplesby unsupervised clustering (FIG. 2c ). These data provide evidence thatPCATs serve as biomarkers for prostate cancer and novel prostate cancersubtypes. Clustering analyses using novel ncRNA outliers also providedisease subtypes (FIG. 16).

Confirmation and Tissue-Specificity of ncRNAs

Validation studies were performed on 14 unannotated expressed regions,including ones both included and not present in the list ofdifferentially expressed transcripts. Reverse transcription PCR (RT-PCR)and quantitative real-time PCR (qPCR) experiments demonstrated a ˜78%(11/14) validation rate in predicted cell line models for bothtranscript identity and expression level (FIG. 17). Next, threetranscripts (PCAT-109, PCAT-14, and PCAT-43) selectively upregulated inprostate cancer compared to normal prostate were examined. From thesequencing data, each genomic loci shows significantly increasedexpression in prostate cancer and metastases, except for PCAT-14, whichappears absent in metastases (FIG. 3a-c ). PCAT-109 also ranks as the #5best outlier in prostate cancer, just ahead of ERG (FIG. 2d and Table6). qPCR on a cohort of 14 benign prostates, 47 tumors, and 10metastases confirmed expression of these transcripts (FIG. 3a-c ). Allthree appear to be prostate-specific, with no expression seen in breastor lung cancer cell lines or in 19 normal tissue types (Table 8). Thistissue specificity was not necessarily due to regulation by androgensignaling, as only PCAT-14 expression was induced by treatment ofandrogen responsive VCaP and LNCaP cells with the synthetic androgenR1881, consistent with previous data from this genomic locus (FIG. 18)(Tomlins et al., Nature 448 (7153), 595 (2007); Stavenhagen et al., Cell55 (2), 247 (1988)). PCAT-14, but not PCAT-109 or PCAT-43, also showeddifferential expression when tested on a panel of matched tumor-normalsamples, indicating that this transcript, which is comprised of anendogenous retrovirus in the HERV-K family (Bannert and Kurth, Proc NatlAcad Sci USA 101 Suppl 2, 14572 (2004)), can be used as a somatic markerfor prostate cancer (FIG. 19). 5′ and 3′ rapid amplification of cDNAends (RACE) at this locus revealed the presence of individual viralprotein open reading frames (ORFs) and a transcript splicing togetherindividual ORF 5′ untranslated region (UTR) sequences (FIG. 20). It wasobserved that the top-ranked intergenic ncRNA resided in the chromosome8q24 gene desert nearby to the c-Myc oncogene. This ncRNA, termedPCAT-1, is located on the edge of the prostate cancer susceptibilityregion 240-43 (FIG. 4a ) and is about 0.5 Mb away from c-Myc. Thistranscript is supported by clear peaks in H3K4me3, Acetyl-H3, and RNApolymerase II ChIP-Seq data (FIG. 4b ). The exon-exon junction in celllines was validated by RT-PCR and Sanger sequencing of the junction(FIG. 4c ), and 5′ and 3′ RACE was performed to elucidate transcriptstructure (FIG. 4d ). By this analysis, PCAT-1 is a mariner familytransposase (Oosumi et al., Nature 378 (6558), 672 (1995); Robertson etal., Nat Genet 12 (4), 360 (1996)) interrupted by an Alu retrotransposonand regulated by a viral long terminal repeat (LTR) promoter region(FIG. 4d and FIG. 21). By qPCR, PCAT-1 expression is specific toprostate tissue, with striking upregulation in prostate cancers andmetastases compared to benign prostate tissue (FIG. 4e ). PCAT-1 ranksas the second best overall prostate cancer biomarker, just behind AMACR(Table 3), indicating that this transcript is a powerful discriminatorof this disease. Matched tumor normal pairs similarly showed markedupregulation in the matched tumor samples (FIG. 4f ). RNA interference(RNAi) was performed in VCaP cells using custom siRNAs targeting PCAT-1sequences and no change in the cell proliferation or invasion uponPCAT-1 knockdown was observed (FIG. 22)

Selective Re-Expression of Repetitive Elements in Cancer

The presence of repetitive elements in PCAT-1 led to an exploration ofrepetitive elements. Repetitive elements, such as Alu and LINE-1retrotransposons, are broadly known to be degenerate in humans (Oosumiet al, supra; Robertson et al., supra; Cordaux et al., Nat Rev Genet 10(10), 691 (2009), with only ˜100 LINE-1 elements (out of 12 500,000)showing possible retrotransposon activity (Brouha et al., Proc Natl AcadSci USA 100 (9), 5280 (2003)). While transcription of these elements isfrequently repressed through DNA methylation and repressive chromatinmodifications (Slotkin and Martienssen, Nat Rev Genet 8 (4), 272(2007)), in cancer widespread hypomethylation has been reported (Cho etal., J Pathol 211 (3), 269 (2007); Chalitchagorn et al., Oncogene 23(54), 8841 (2004); Yegnasubramanian et al., Cancer Res 68 (21), 8954(2008)). Moreover, recent evidence indicates that these elements havefunctional roles in both normal biology (Kunarso et al., Nat Genet.) andcancer (Lin et al., Cell 139 (6), 1069 (2009)), even if their sequenceshave mutated away from their evolutionary ancestral sequence (Chow etal., Cell 141 (6), 956). To date, only RNA-Seq platforms enablediscovery and quantification of specific transposable elements expressedin cancer. As described above, it was observed that >50% of unannotatedexons in the assembly overlap with at least one repetitive element (FIG.11). Since these elements pose mappability challenges when performingtranscriptome assembly with unique reads, these loci typically appear as“mountain ranges” of expression, with uniquely mappable regions formingpeaks of expression separated by unmappable “ravines” (FIGS. 23 and 24).PCR and Sanger sequencing experiments were performed to confirm thatthese transposable elements of low mappability are expressed as part ofthese loci (FIGS. 23 and 24). To probe this observation further, theexons from unannotated transcripts in the assembly, with the addition ofthe flanking 50, 100, or 500 bp of additional genomic sequence to the 5′and 3′ end of the exons were generated, the overlap of these intervalswith repetitive elements to randomly permuted genomic intervals ofsimilar sizes was performed. A highly significant enrichment forrepetitive elements in the dataset was observed (OR 2.82 (95% CI2.68-2.97), p<10-100, Table 9). Examination of the individual repetitiveelement classes revealed a specific enrichment for SINE elements,particularly Alus (p≦2×10-16, Tables 10 and 11). A subset of LINE-1 andAlu transposable elements demonstrate marked differential expression ina subset of prostate cancer tumors (FIG. 25). One locus on chromosome 2(also highlighted in FIG. 3b ) is a 500+kb region with numerousexpressed transposable elements (FIG. 26). This locus, termed SecondChromosome Locus Associated with Prostate-1 (SChLAP1), harborstranscripts that perform extremely well in outlier analyses for prostatecancer (Tables 6 and 7). PCAT-109, discussed above, is one outliertranscript in this region. Moreover, the SChLAP1 locus is highlyassociated with patients positive for ETS gene fusions (p<0.0001,Fisher's exact test, FIG. 27), whereas this association was not observedwith other expressed repeats. A direct regulatory role for ERG on thisregion was not identified using siRNA-mediated knockdown of ERG in theVCaP cell line. These data indicate that the dysregulation of repeats incancer is highly specific, and that this phenomenon associates with onlya subset of tumors and metastases. Thus, the broad hypomethylation ofrepeat elements observed in cancer (Cho et al., J Pathol 211 (3), 269(2007); Chalitchagorn et al., Oncogene 23 (54), 8841 (2004);Yegnasubramanian et al., Cancer Res 68 (21), 8954 (2008)) does notaccount for the high specificity of repeat expression.

Non-Invasive Detection of ncRNAs in Urine

Taken together, these data show an abundance of novel ncRNA biomarkersfor prostate cancer, many of which appear to have tissue specificity. 77urine sediments obtained from patients with prostate cancer and 31control patients without known disease (Table 12 for sample details)were analyzed (Laxman et al., Cancer Res 68 (3), 645 (2008)). Thecontrol patients are defined as those lacking cancer histology uponprostate biopsy and lacking the TMPRSS2-ERG fusion transcript in urinesediment RNA (Laxman et al., supra). PCAT-1 and PCAT-14, as well as theknown ncRNA biomarker PCA3, were selected for evaluation on this urinepanel due to their biomarker status in patient tissue samples. qPCRanalysis led to an observation of specificity in their ability to detectprostate cancer patients and not patients with normal prostates (FIG.5a-c ). In several cases, patients with ETS-negative prostate cancerthat were misclassified as “benign” are clearly evident (FIGS. 5a and 5c). Moreover, PCAT-14 appears to perform almost as well as PCA3 as aurine biomarker, nearly achieving statistical significance (p=0.055,Fisher's exact test) despite the small number of patients used for thispanel. It was next evaluated whether these unannotated ncRNAs identifieda redundant set of patients that would also be identified by other urinetests, such as PCA3 or TMPRSS2-ERG transcripts. Comparing PCAT-1 andPCAT-14 expression in urine samples to PCA3 or to each other revealedthat these ncRNAs identified distinct patient sets, indicating that apatient's urine typically harbors PCAT-1 or PCAT-14 transcripts but notboth (FIG. 5d ). Using the cut-offs displayed in FIG. 5a-c , a binaryheatmap comparing these three ncRNAs with patients' TMPRSS2-ERG statuswas generated (FIG. 5e ). The ncRNAs were able to detect additionalETS-negative patients with prostate cancer through this urine test,indicating that they have clinical utility as highly specific markersfor prostate cancer using a multiplexed urine test. Combining PCAT-1,PCAT-14 and PCA3 into a single “non-coding RNA signature” generated ahighly specific urine signature (p=0.0062, Fisher's exact test, FIG. 5f) that identifies a number of prostate cancer patients that is broadlycomparable to the TMPRSS2-ERG fusion (33% vs. 45%).

FIG. 34 shows detection of prostate cancer RNAs in patient urine samplesusing qPCR. All RNA species were detectable in urine. FIG. 35 shows thatmultiplexing urine SChLAP-1 measurements with serum PSA improvesprostate cancer risk stratification. Individually, SChLAP-1 is apredictor for prostate cancers with intermediate or high clinical riskof aggressiveness. Multiplexing this measurement with serum PSA improvesupon serum PSA's ability to predict for more aggressive disease.

Additional Characterization

Additional experiments were conducted related to PCAT-1 and SChLAP-1region in prostate cancer. FIG. 29 demonstrates that PCAT-1 expressionsensitizes prostate cancer cells to treatment with PARP-1 inhibitors.FIG. 30 demonstrates that PCAT-1 expression sensitizes prostate cells toradiation treatment.

FIG. 31 demonstrates that unannotated intergenic transcripts in SChLAP-1differentiate prostate cancer and benign samples. FIG. 32 demonstratesthat SChLAP-1 is required for prostate cancer cell invasion andproliferation. Prostate cell lines, but not non-prostate cells, showed areduction in invasion by Boyden chamber assays. EZH2 and non-targetingsiRNAs served as positive and negative controls, respectively. Deletionanalysis of SChLAP-1 was performed. FIG. 33 shows that a regionessentialfor its function was identified.

ncRNAs in Lung, Breast, and Pancreatic Cancers

Analysis of the lung cancer transcriptome (FIG. 36) was performed. 38lung cell lines were analyzed by RNA-Seq and then lncRNA transcriptswere reconstructed. Unannotated transcripts accounted for 27% of alltranscripts. Novel transcripts well more highly expressed than annotatedncRNAs but not protein-coding transcripts. An outlier analyses of 13unannotated transcripts shows novel lncRNAs in subtypes of lung cancercell lines. FIG. 37 shows discovery of M41 and ENST-75 ncRNAs in lungcancer. FIG. 38 shows that lncRNAs are drivers and biomarkers in lungcancer. FIG. 39 shows identification of cancer-associated lncRNAs inbreast and pancreatic cancer. Three novel breast cancer lncRNAs werenominated from RNA-Seq data (TU0011194, TU0019356, and TU0024146. Allshow outlier expression patterns in breast cancer samples but not benignsamples. Three novel pancreatic cancer lncRNAs were nominated fromRNA-Seq data (TU0009141, TU0062051, and TU0021861). All show outlierexpression patterns in pancreatic cancer samples but not benign samples.

TABLE 1 TopHat TopHat Library ID Sample Name Type Sample Type Read TypeRead Length Total Reads (x2 for PE) Mapped Reads Splice Junction Reads %Splice Diagnosis ETS status ctp_42808AAXX_2 PWR-1E RNA-Seq CellLinepaired_end 40 7363045 8367325 1091179 13.04% Benign Negativemctp_30CYNAAXX_5 prEC RNA-Seq Cell Line single_read 40 3078462 955130107311 11.24% Benign Negative mctp_209ENAAXX_8 prEC RNA-Seq Cell Linesingle_read 30 3319066 871560 67610 7.76% Benign Negativemctp_314T1AAXX_1 prEC RNA-Seq Cell Line paired_end 40 7748627 7443379747751 10.05% Benign Negative mctp_30351AAXX_7 prEC RNA-Seq Cell Linepaired_end 40 5853459 9562343 892380 9.33% Benign Negativemctp_314T1AAXX_2 PrSMC RNA-Seq Cell Line paired_end 40 8465529 8626281935503 10.84% Benign Negative mctp_20E5CAAXX_6 RWPE RNA-Seq Cell Linesingle_read 36 5300138 1693464 149383 8.82% Benign Negativemctp_20E6CAAXX_7 RWPE RNA-Seq Cell Line single_read 36 5347764 1710762250130 8.78% Benign Negative mctp_20E6CAAXX_8 RWPE RNA-Seq Cell Linesingle_read 36 4778245 1539225 135996 8.84% Benign Negativemctp_20F05AAXX_6 RWPE RNA-Seq Cell Line single_read 36 4833510 1565250137416 8.78% Benign Negative mctp_20F0BAAXX_7 RWPE RNA-Seq Cell Linesingle_read 36 5005497 1622033 143105 8.83% Benign Negativemctp_20F0BAAXX_8 RWPE RNA-Seq Cell Line single_read 36 4955663 1607124141358 8.80% Benign Negative mctp_20F0GAAXX_7 RWPE RNA-Seq Cell Linesingle_read 36 4866138 1568635 130224 8.81% Benign Negativemctp_20F0GAAXX_8 RWPE RNA-Seq Cell Line single_read 36 4809235 1550957156049 8.77% Benign Negative mctp_20F0GAAXX_6 RWPE RNA-Seq Cell Linesingle_read 36 4901167 1580424 138674 8.77% Benign Negativemctp_4250BAAXX_3 WPMY-1 RNA-Seq Cell Line paired_end 40 7593911 81033031011035 12.48% Benign Negative mctp_20F69AAXX_1 22Rv1 RNA-Seq Cell Linesingle_read 36 5301735 2345205 169257 7.22% Localized Negativemctp_31401AAXX_6 22Rv1 RNA-Seq Cell Line paired_end 40 9214120 95006161063132 11.07% Localized Negative mctp_429T4AAXX_5 CA-HPV.10 RNA-SeqCell Line paired_end 40 13654861 14731620 1750416 11.88% LocalizedNegative mctp_42974AAXX_7 CWR22 RNA-Seq Cell Line paired_end 40 1388298414791235 1530790 10.35% Localized Negative mctp_30DJDAAXX_2 VCaP RNA-SeqCell Line single_read 45 8175900 1400658 167748 11.98% Metastatic ERG+mctp_20CCAAAXX_7 VCaP RNA-Seq Cell Line single_read 36 5372814 98120489660 9.14% Metastatic ERG+ mctp_20CCAAAXX_6 VCaP RNA-Seq Cell Linesingle_read 36 5210292 957549 86199 9.00% Metastatic ERG+mctp_20CCAAAXX_4 VCaP RNA-Seq Cell Line single_read 36 5220542 95662288342 9.23% Metastatic ERG+ mctp_20CCAAAXX_3 VCaP RNA-Seq Cell Linesingle_read 36 5405126 988972 96075 9.11% Metastatic ERG+mctp_20CCAAAXX_2 VCaP RNA-Seq Cell Line single_read 36 5091526 93827285147 9.07% Metastatic ERG+ mctp_20CCAAAXX_1 VCaP RNA-Seq Cell Linesingle_read 36 4273325 804080 72804 9.05% Metastatic ERG+mctp_20E5CAAXX_1 VCaP RNA-Seq Cell Line single_read 36 4717324 86185678164 9.07% Metastatic ERG+ mctp_20CCAAAXX_8 VCaP RNA-Seq Cell Linesingle_read 36 5024204 976214 85535 9.23% Metastatic ERG+mctp_207D6AAXX_2 VCaP RNA-Seq Cell Line single_read 36 4491727 80799773610 9.11% Metastatic ERG+ mctp_429T4AAXX_4 NCI-H660 RNA-Seq Cell Linepaired_end 40 12322606 15104197 1377708 9.12% Metastatic ERG+mctp_20FDGAAXX_4 LNCaP RNA-Seq Cell Line single_read 36 5109105 1430548119570 8.35% Metastatic ETV1+ mctp_20F0GAAXX_1 LNCaP RNA-Seq Cell Linesingle_read 36 5015345 1402514 117293 8.36% Metastatic ETV1+mctp_20F0GAAXX_3 LNCaP RNA-Seq Cell Line single_read 36 5106724 1426054119462 8.57% Metastatic ETV1+ mctp_20F0GAAXX_2 LNCaP RNA-Seq Cell Linesingle_read 36 4990256 1398161 117850 8.43% Metastatic ETV1+mctp_20E6CAAXX_2 LNCaP RNA-Seq Cell Line single_read 36 4593789 1370920112874 8.30% Metastatic ETV1+ mctp_20E6CAAXX_3 LNCaP RNA-Seq Cell Linesingle_read 36 5432666 1510040 126177 5.96% Metastatic ETV1+mctp_20E6CAAXX_4 LNCaP RNA-Seq Cell Line single_read 36 4553947 1501247112409 3.62% Metastatic ETV1+ mctp_42PMUAAXX_6 LNCaP CDS2 RNA-Seq CellLine paired_end 38 10714839 10272130 1057574 10.30% Metastatic Negativemctp_42PMUAAXX_7 LNCaP CDS3 RNA-Seq Cell Line paired_end 38 56134739586206 973617 10.16% Metastatic Negative mctp_42TA8AAXX_7 DU-145RNA-Seq Cell Line paired_end 38 13804352 13651384 1372507 10.04%Metastatic Negative mctp_42TA8AAXX_6 DU-145 RNA-Seq Cell Line paired_end38 15785849 15918091 1570336 9.86% Metastatic Negative mctp_42TA8AAXX_5DU-145 RNA-Seq Cell Line paired_end 38 14197743 14950079 1485534 9.93%Metastatic Negative mctp_42TA8AAXX_3 DU-145 RNA-Seq Cell Line paired_end38 12152298 13047548 1320224 10.12% Metastatic Negative mctp_42TA8AAXX_2DU-145 RNA-Seq Cell Line paired_end 38 12583744 13715578 1384118 10.09%Metastatic Negative mctp_42TA8AAXX_1 DU-145 RNA-Seq Cell Line paired_end38 10944533 6437207 653992 10.16% Metastatic Negative mctp_42TBDAAXX_8DU-145 RNA-Seq Cell Line paired_end 38 9229144 10026773 1013731 10.11%Metastatic Negative mctp_42PFAAAXX_6 LNCaP CD5 RNA-Seq Cell Linepaired_end 38 12368574 9518829 966541 10.15% Metastatic Negative parentmctp_42PFAAAXX_5 LNCaP CDS1 RNA-Seq Cell Line paired_end 38 1448986813995752 1611356 10.08% Metastatic Negative mctp_20BC5AAXX_8 DU-145RNA-Seq Cell Line single_read 36 5351406 1568641 235883 9.13% MetastaticNegative mctp_20F69AAXX_2 DU-145 RNA-Seq Cell Line single_read 365069249 2437193 225574 9.25% Metastatic Negative mctp_3001DAAXX_3 DU-145RNA-Seq Cell Line single_read 45 8586532 4162580 498466 11.97%Metastatic Negative mctp_429T4AAXX_3 LAPC-4 RNA-Seq Cell Line paired_end40 14725826 16711055 1790200 10.71% Metastatic Negative mctp_3064YAAXX_1PC3 RNA-Seq Cell Line paired_end 40 10267396 10291560 1185473 11.52%Metastatic Negative mctp_20F69AAXX_3 PC3 RNA-Seq Cell Line single_read36 5364050 2547308 237597 8.33% Metastatic Negative mctp_429T4AAXX_2C4-2B RNA-Seq Cell Line paired_end 40 12754909 12823209 1591197 12.41%Metastatic Negative mctp_429T4AAXX_6 MDA FCa 2b RNA-Seq Cell Linepaired_end 40 13341323 14909946 1634544 10.96% Metastatic Negativemctp_42808AAXX_4 WPE1-NB26 RNA-Seq Cell Line paired_end 40 105939209930521 1240048 12.49% Metastatic Negative mctp_42848AAXX_4 PrBe10013RNA-Seq Tissue paired_end 40 15313195 18040527 1435670 7.96% BenignNegative mctp_30WUZAAXX_5 PrBe10013 RNA-Seq Tissue paired_end 38 982274412263152 927590 7.56% Benign Negative mctp_42848AAXX_8 PrBe10014 RNA-SeqTissue paired_end 40 11242542 9036870 715431 7.92% Benign Negativemctp_42PFAAAXX_2 PrBe10014 RNA-Seq Tissue paired_end 38 6616551 6359875471003 7.38% Benign Negative mctp_30WUZAAXX_5 PrBe10014 RNA-Seq Tissuepaired_end 38 3977109 4235690 321691 7.56% Benign Negativemctp_42CUAAXX_7 PrBe10015 RNA-Seq Tissue paired_end 40 7584480 7927754632270 7.90% Benign Negative mctp_42NY4AAXX_2 PrBe10015 RNA-Seq Tissuepaired_end 38 14331227 12877894 936438 7.27% Benign Negativemctp_42543AAXX_1 PrBe10016 RNA-Seq Tissue paired_end 40 1212229411750631 820710 6.98% Benign Negative mctp_42NY9AAXX_3 PrBe10016 RNA-SeqTissue paired_end 38 11809596 11367863 741980 6.53% Benign Negativemctp_30WUZAAXX_7 PrBe10017 RNA-Seq Tissue paired_end 38 1859890 2156367152020 7.05% Benign Negative mctp_420JFAAXX_5 PrBe10017 RNA-Seq Tissuepaired_end 40 14245213 14383797 1025161 7.13% Benign Negativemctp_43830AAXX_5 PrBe10018 RNA-Seq Tissue paired_end 38 1681639317002418 1465145 8.62% Benign Negative mctp_42NY4AAXX_6 PrBe10018RNA-Seq Tissue paired_end 38 15877894 16489882 1418434 8.60% BenignNegative mctp_42D3MAAXX_5 aN10_6 RNA-Seq Tissue paired_end 40 1010295811948284 938291 7.85% Benign Negative mctp_3054YAAXX_2 aN11_1 RNA-SeqTissue paired_end 40 9792955 10708088 843013 7.88% Benign Negativemctp_42P6UAAXX_1 aN11_1 RNA-Seq Tissue paired_end 40 14658825 10917481823116 7.54% Benign Negative mctp_3040WAAXX_1 aN13_2 RNA-Seq Tissuepaired_end 40 14755517 15347535 1174999 7.66% Benign Negativemctp_42P6GAAXX_4 aN13_2 RNA-Seq Tissue paired_end 40 16107801 160705651231834 7.67% Benign Negative mctp_3G54YAAXX_3 aN14_4 RNA-Seq Tissuepaired_end 40 9282092 9526550 733492 7.70% Benign Negativemctp_42P6UAAXX_2 aN14_4 RNA-Seq Tissue paired_end 40 12317092 11968962894313 7.47% Benign Negative mctp_30653AAXX_5 PrBe10002 RNA-Seq Tissuepaired_end 40 10282216 3480927 190504 8.47% Benign Negativemctp_30CVWAAXX_6 PrBe10002 RNA-Seq Tissue single_read 40 4389340 87714639125 4.45% Benign Negative mctp_3GCYWAAXX_7 PrBe10003 RNA-Seq Tissuesingle_read 40 4724195 382030 17102 4.48% Benign Negativemctp_42P6UAAXX_5 aN15_3 RNA-Seq Tissue paired_end 40 14035929 10890695928050 8.53% Benign Negative mctp_3054YAAXX_7 aN15_3 RNA-Seq Tissuepaired_end 40 8772663 8101379 714429 8.82% Benign Negativemctp_30CM2AAXX_6 aN23 RNA-Seq Tissue single_read 35 6359089 2998000171398 5.72% Benign Negative mctp_30CM2AAXX_4 aN25 RNA-Seq Tissuesingle_read 35 5162304 2181784 100935 4.63% Benign Negativemctp_30CM2AAXX_5 aN25 RNA-Seq Tissue single_read 35 5667482 2632682123775 4.70% Benign Negative mctp_30CM3AAXX_1 aN27 RNA-Seq Tissuesingle_read 35 4771661 1836620 93266 5.02% Benign Negativemctp_30CM2AAXX_2 aN27 RNA-Seq Tissue single_read 35 5843509 2090978103544 4.95% Benign Negative mctp_30CM2AAXX_7 aN29 RNA-Seq Tissuesingle_read 35 5661652 1555510 87547 5.63% Benign Negativemctp_30CM2AAXX_5 aN29 RNA-Seq Tissue single_read 35 5201944 147297583465 5.67% Benign Negative mctp_ZCFCKAAXX_1 aN31 RNA-Seq Tissuesingle_read 36 4206556 1642681 122140 7.44% Benign Negativemctp_ZCFCKAAXX_2 aN31 RNA-Seq Tissue single_read 35 3624043 1504320107996 7.18% Benign Negative mctp_ZCFCKAAXX_4 aN32 RNA-Seq Tissuesingle_read 36 4145596 1866001 118140 6.35% Benign Negativemctp_ZCFCKAAXX_3 aN32 RNA-Seq Tissue single_read 36 4352455 1835242115876 6.31% Benign Negative mctp_ZCFCKAAXX_7 aN33 RNA-Seq Tissuesingle_read 35 5375947 2024782 122564 6.05% Benign Negativemctp_ZCFCKAAXX_8 aN33 RNA-Seq Tissue single_read 35 3974268 158786996704 6.09% Benign Negative mctp_42D3MAAXX_5 aT12_4 RNA-Seq Tissuepaired_end 40 10323732 10700518 891873 8.34% Localized ERG+mctp_42P6UAAXX_6 aT12_4 RNA-Seq Tissue paired_end 40 12591851 126873291035642 8.16% Localized ERG+ mctp_2GACMAAXX_7 aT54 RNA-Seq Tissuesingle_read 35 4951150 2395362 153160 6.39% Localized ERG+mctp_3050WAAXX_3 aT5_5 RNA-Seq Tissue paired_end 40 14290078 151579101231918 6.13% Localized ERG+ mctp_20AGMAAXX_8 aT62 RNA-Seq Tissuesingle_read 35 5144018 2594526 146853 5.66% Localized ERG+mctp_20G93AAXX_1 aT76 RNA-Seq Tissue single_read 30 4482645 209539077035 3.68% Localized ERG+ mctp_4203NAAXX_2 aT8_2 RNA-Seq Tissuepaired_end 40 5949944 10269470 745408 7.26% Localized ERG+mctp_42P6UAAXX_7 aT2_2 RNA-Seq Tissue paired_end 40 13165443 12758016925564 7.25% Localized ERG+ mctp_2GACMAAXX_6 aT20 RNA-Seq Tissuesingle_read 35 4905934 2380289 168032 7.06% Localized ETV1+mctp_30Y5NAAXX_6 aT52 RNA-Seq Tissue paired_end 34 9555248 11236237579321 5.16% Localized ETV1+ mctp_20593AAXX_4 PrCa10001 RNA-Seq Tissuesingle_read 30 5073375 2003723 81777 4.05% Localized Negativemctp_30CVWAAXX_2 PrCa10002 RNA-Seq Tissue single_read 40 3979845 1573898142307 9.04% Localized Negative mctp_20G95AAXX_7 PrCa10002 RNA-SeqTissue single_read 30 5337734 2185509 134758 6.17% Localized Negativemctp_30CW7AAXX_4 PrCa10003 RNA-Seq Tissue single_read 40 7245088 3325480200975 6.04% Localized Negative mctp_30CVWAAXX_1 PrCa10003 RNA-SeqTissue single_read 40 2232676 996717 47049 4.72% Localized Negativemctp_20G93AAXX_6 PrCa10003 RNA-Seq Tissue single_read 30 4209584 186053180219 4.29% Localized Negative mctp_20G93AAXX_2 PrCa10004 RNA-Seq Tissuesingle_read 30 4877618 2429172 101279 4.17% Localized Negativemctp_30CW2AAXX_3 PrCa10004 RNA-Seq Tissue single_read 40 8502651 4337032261531 5.03% Localized Negative mctp_20G93AAXX_1 PrCa10006 RNA-SeqTissue single_read 30 4697349 2219408 86343 3.09% Localized Negativemctp_30CW2AAXX_5 PrCa10006 RNA-Seq Tissue single_read 40 7780464 3825883211003 5.52% Localized Negative mctp_30WU2AAXX_6 PrCa10013 RNA-SeqTissue paired_end 38 7094073 8465055 698526 8.25% Localized Negativemctp_42FFAAAXX_3 PrCa10013 RNA-Seq Tissue paired_end 38 1312995014850397 1205327 8.12% Localized Negative mctp_42CJFAAXX_4 PrCa10013RNA-Seq Tissue paired_end 40 11855634 13593367 1193752 8.78% LocalizedNegative mctp_42603AAXX_5 PrCa10014 RNA-Seq Tissue paired_end 4011559996 11278990 923485 8.19% Localized Negative mctp_42808AAXX_1PrCa10014 RNA-Seq Tissue paired_end 40 9629325 7576252 705179 9.31%Localized Negative mctp_42CJ1AAXX_5 PrCa10014 RNA-Seq Tissue paired_end40 15108424 17200396 1326961 7.71% Localized Negative mctp_30WU2AAXX_1PrCa10014 RNA-Seq Tissue paired_end 38 13033345 15792364 1122174 7.11%Localized Negative mctp_42543AAXX_3 PrCa10015 RNA-Seq Tissue paired_end40 14322439 14744516 1043963 7.08% Localized Negative mctp_30WUJAAXX_4PrCa10015 RNA-Seq Tissue paired_end 38 9081533 10010115 675880 6.75%Localized Negative mctp_42NY4AAXX_4 PrCa10016 RNA-Seq Tissue paired_end38 11879138 13526717 954576 7.06% Localized Negative mctp_42843AAXX_6PrCa10016 RNA-Seq Tissue paired_end 40 11883518 13459171 1027559 7.63%Localized Negative mctp_42843AAXX_2 PrCa10017 RNA-Seq Tissue paired_end40 7583235 7555611 622237 8.24% Localized Negative mctp_429FAAAXX_1PrCa10017 RNA-Seq Tissue paired_end 38 13554764 11318051 852274 7.53%Localized Negative mctp_42NY4AAXX_5 PrCa10018 RNA-Seq Tissue paired_end38 16107721 18636010 1471850 7.90% Localized Negative mctp_42CJFAAXX_2PrCa10018 RNA-Seq Tissue paired_end 40 12506692 14935573 1501243 8.71%Localized Negative mctp_30V5NAAXX_4 PrCa10018 RNA-Seq Tissue paired_end34 8565125 10521603 649435 6.17% Localized Negative mctp_42CUAAXX_8PrCa10019 RNA-Seq Tissue paired_end 40 14204491 12235106 884253 7.23%Localized Negative mctp_42543AAXX_5 PrCa10021 RNA-Seq Tissue paired_end40 14583654 15470222 1147556 7.42% Localized Negative mctp_42CJFAAXX_1PrCa10023 RNA-Seq Tissue paired_end 40 9473417 11040935 939157 8.51%Localized Negative mctp_42CUAAXX_6 PrCa10024 RNA-Seq Tissue paired_end40 5249645 5541745 432904 7.81% Localized Negative mctp_42PF0AAXX_3PrCa10024 RNA-Seq Tissue paired_end 38 8109134 7508966 541558 7.21%Localized Negative mctp_42C16AAXX_3 PrCa10028 RNA-Seq Tissue paired_end40 5344368 6256991 516414 6.25% Localized Negative mctp_42T69AAXX_5PrCa10030 RNA-Seq Tissue paired_end 38 17239720 18212019 1265021 6.95%Localized Negative mctp_42T89AAXX_1 PrCa10031 RNA-Seq Tissue paired_end38 17881940 19792732 1356072 5.85% Localized Negative mctp_42T69AAXX_6PrCa10032 RNA-Seq Tissue paired_end 38 16892184 18313947 1420306 7.75%Localized Negative mctp_42T69AAXX_2 PrCa10033 RNA-Seq Tissue paired_end38 10736010 7148288 460799 6.45% Localized Negative mctp_42T89AAXX_7PrCa10034 RNA-Seq Tissue paired_end 38 16494766 18616451 1416932 7.61%Localized Negative mctp_42P0UAAXX_5 aT1_3 RNA-Seq Tissue paired_end 4014031093 15128363 1089323 7.20% Localized Negative mctp_302XWAAXX_2aT1_3 RNA-Seq Tissue paired_end 40 14017921 15424771 1120415 7.26%Localized Negative mctp_42543AAXX_7 aT38 RNA-Seq Tissue paired_end 4014028075 14206815 1075647 7.57% Localized Negative mctp_50V5NAAXX_3 aT38RNA-Seq Tissue paired_end 34 9148041 10857079 634116 5.85% LocalizedNegative mctp_42Y27AAXX_2 aT42 RNA-Seq Tissue paired_end 38 1590773917336906 1111429 6.41% Localized Negative mctp_30GJ0AAXX_5 aT41 RNA-SeqTissue single_read 45 9446722 4597917 345881 7.52% Localized Negativemctp_42Y2TAAXX_3 aT45 RNA-Seq Tissue paired_end 38 16395435 13748230814457 5.92% Localized Negative mctp_300JQAAXX_6 aT45 RNA-Seq Tissuesingle_read 45 9154922 3918914 273181 6.97% Localized Negativemctp_32503AAXX_7 aT53 RNA-Seq Tissue paired_end 40 12164542 130400821055172 8.09% Localized Negative mctp_20F66AAXX_6 aT56 RNA-Seq Tissuesingle_read 36 4655382 2002111 109234 5.46% Localized Negativemctp_300WTAAXX_2 aT56 RNA-Seq Tissue single_read 40 7386627 3040283189576 5.22% Localized Negative mctp_20F85AAXX_1 aT56 RNA-Seq Tissuesingle_read 36 4894127 1958986 108306 5.50% Localized Negativemctp_30U09AAXX_4 aT57 RNA-Seq Tissue paired_end 40 9490697 9403761688415 7.52% Localized Negative mctp_420JFAAXX_8 aT58 RNA-Seq Tissuepaired_end 40 4160283 4703591 386748 8.22% Localized Negativemctp_42500AAXX_5 aT61 RNA-Seq Tissue paired_end 40 10252280 10445106718210 6.88% Localized Negative mctp_20F66AAXX_7 aT56 RNA-Seq Tissuesingle_read 36 5016117 2455183 153987 6.27% Localized Negativemctp_300W7AAXX_1 aT56 RNA-Seq Tissue single_read 40 8055624 3791022268911 7.09% Localized Negative mctp_20F85AAXX_2 aT56 RNA-Seq Tissuesingle_read 36 5184870 2368556 149558 6.51% Localized Negativemctp_42P5UAAXX_8 aT6_1 RNA-Seq Tissue paired_end 40 936249 998194 766987.88% Localized Negative mctp_420JFAAXX_7 aT6_1 RNA-Seq Tissuepaired_end 40 9428987 7353536 524419 7.13% Localized Negativemctp_42FFAAAXX_4 aT6_1 RNA-Seq Tissue paired_end 38 13242928 9178336610189 6.65% Localized Negative mctp_300W3AAXX_7 PrCa10007 RNA-SeqTissue single_read 42 7909935 3246264 305730 8.36% Localized Negativemctp_4203NAAXX_2 PrCa10025 RNA-Seq Tissue paired_end 40 8614803 9085984903098 9.94% Localized Negative mctp_4202NAAXX_1 PrCa10026 RNA-SeqTissue paired_end 40 7781206 8539677 801237 9.38% Localized Negativemctp_4203NAAXX_3 PrCa10027 RNA-Seq Tissue paired_end 40 1030538211427244 1110643 9.72% Localized Negative mctp_42T89AAXX_4 PrCa10029RNA-Seq Tissue paired_end 38 8674521 9910831 734269 7.41% LocalizedNegative mctp_42Y6WAAXX_6 PrCa10029 RNA-Seq Tissue paired_end 3813229893 14068633 1060520 7.54% Localized Negative mctp_3064YAAXX_4ULM2927 RNA-Seq Tissue paired_end 40 9542506 8623117 638903 7.41%Localized Negative mctp_4283YAAXX_4 aT47 RNA-Seq Tissue paired_end 407806523 7010780 354081 5.05% Localized Negative mctp_2GF06AAXX_3 aM23RNA-Seq Tissue single_read 36 4680305 2018538 116179 5.67% MetastaticERG+ mctp_2GF66AAXX_4 aM23 RNA-Seq Tissue single_read 36 4913495 2187836127972 5.85% Metastatic ERG+ mctp_20F69AAXX_4 aM28 RNA-Seq Tissuesingle_read 36 5374538 2103543 99339 4.51% Metastatic ERG+mctp_20LV8AAXX_6 aM28 RNA-Seq Tissue single_read 30 5517555 223452979073 3.54% Metastatic ERG+ mctp_20LV8AAXX_7 aM28 RNA-Seq Tissuesingle_read 30 5548780 2250821 80015 3.55% Metastatic ERG+mctp_20AGMAAXX_4 aM29 RNA-Seq Tissue single_read 36 4903432 183976773792 4.01% Metastatic ERG+ mctp_20FETAAXX_6 aM29 RNA-Seq Tissuesingle_read 36 5092573 1777721 73464 4.13% Metastatic ERG+mctp_2074VAAXX_1 aM38 RNA-Seq Tissue single_read 36 5126432 2559949150938 5.90% Metastatic ERG+ mctp_30CVMAAXX_4 aM38 RNA-Seq Tissuesingle_read 40 4759734 2287003 139731 6.11% Metastatic ERG+mctp_30TVGAAXX_3 aM38 RNA-Seq Tissue paired_end 40 6778935 3689892280553 7.60% Metastatic ERG+ mctp_43620AAXX_6 aM15 RNA-Seq Tissuepaired_end 38 13825315 11684425 950874 8.14% Metastatic ERG+mctp_3074VAAXX_3 aM15 RNA-Seq Tissue single_read 36 4744456 208767095102 4.56% Metastatic ERG+ mctp_3074VAAXX_5 aM37 RNA-Seq Tissuesingle_read 36 4509553 1941952 91631 4.72% Metastatic ETV1+mctp_305KAAAXX_2 aM41 RNA-Seq Tissue single_read 36 4480735 170201974579 4.38% Metastatic ETV1+ mctp_20FETAAXX_8 aM41 RNA-Seq Tissuesingle_read 36 5372905 2091694 82686 4.03% Metastatic ETV1+mctp_2074VAAXX_2 aM41 RNA-Seq Tissue single_read 36 5222746 218403088780 4.06% Metastatic ETV1+ mctp_3064VAAXX_6 ULM811239- RNA-Seq Tissuepaired_end 40 9653726 10247077 1004315 9.80% Metastatic Negative 97mctp_3064VAAXX_5 ULM82440-97 RNA-Seq Tissue paired_end 40 982227010358561 951893 9.19% Metastatic Negative mctp_20E2PAAXX_7 aM11 RNA-SeqTissue single_read 36 5201588 2333757 100570 4.65% Metastatic Negativemctp_42CJFAAXX_6 aM20 RNA-Seq Tissue paired_end 40 9038499 8821509572135 6.49% Metastatic Negative mctp_20EXPAAXX_6 aM36 RNA-Seq Tissuesingle_read 36 5587558 2277795 104747 4.60% Metastatic Negativemctp_30CW7AAXX_6 aM36 RNA-Seq Tissue single_read 40 9198611 3833469193678 5.05% Metastatic Negative mctp_307VGAAXX_1 aM36 RNA-Seq Tissuepaired_end 40 7749518 2430500 141723 5.83% Metastatic Negativemctp_205K4AAXX_1 aM36 RNA-Seq Tissue single_read 36 5097473 2217107126224 5.69% Metastatic Negative mctp_20E7PAAXX_2 aM39 RNA-Seq Tissuesingle_read 36 5516548 235217 113714 4.86% Metastatic Negativemctp_307YGAAXX_5 aM39 RNA-Seq Tissue paired_end 40 6279578 3568922236298 6.62% Metastatic Negative mctp_20FETAAXX_7 aM39 RNA-Seq Tissuesingle_read 36 5354844 2117551 102001 4.82% Metastatic Negativemctp_20E2PAAXX_8 aM43 RNA-Seq Tissue single_read 36 5497785 168008272729 4.33% Metastatic Negative mctp_30CW7AAXX_7 aM43 RNA-Seq Tissuesingle_read 40 8489329 3952621 200213 5.07% Metastatic Negative TOTAL1723713421 1417627939 114448745 8.07%

TABLE 2 Merge intron- Join Filter Classification redundant Informatictranscript intronic UCSC Chromosome Cuffcompare tree filter transcriptsfilters fragments pre-mRNA Canonical Refseq chr1 759121 272072 127015030 4489 3652 2499 3334 chr2 581574 206281 9353 3224 2856 2361 15792023 chr3 518621 167071 5706 2917 2560 2053 1312 1816 chr4 329950 1031135160 2019 1731 1444 977 1238 chr5 380613 126139 5833 2365 2067 1694 11041465 chr6 396848 145607 7580 2590 2309 1874 1370 1667 chr7 432152 1340516432 2355 2132 1703 1326 1583 chr8 308935 97724 4226 1729 1529 1243 8481210 chr9 359300 122626 4069 1937 1767 1402 1114 1272 chr10 354625103512 3509 1672 1508 1226 998 1382 chr11 424606 165211 6909 2922 26402102 1566 2023 chr12 425280 138650 6872 2653 2373 1858 1233 1668 chr13159649 68284 3616 1118 908 751 425 549 chr14 261497 123741 4842 18061619 1308 855 1102 chr15 291241 108058 5816 1884 1626 1321 1362 1127chr16 364747 124182 3968 2002 1835 1386 1093 1311 chr17 473261 1684695581 2780 2582 1950 1480 1907 chr18 144300 49112 2504 785 682 539 377459 chr19 494738 189411 7209 3543 3239 2269 1668 2314 chr20 217223 703083059 1243 1158 907 659 926 chr21 113368 29728 939 495 436 354 306 427chr22 223385 73509 2401 1156 1068 798 633 771 chrX 222743 94591 49971516 1349 1161 959 1841 chrY 15190 4039 272 81 71 59 148 254 Total8253710 2885489 123554 49822 44534 35415 25921 33669

TABLE 3 # Uniquely Peak mapped Antibody Antibody Finder reads (in #Peaks GEO ID File name Pubmed ID used vendor Used millions) CalledGSM353631 VCaP_regular_medium_H3K4me1 20478527 ab8895 Abcam MACS 6.9623116 GSM353632 VCaP_regular_medium_H3K4me2 20478527 ab7766 Abcam MACS5.97 74153 GSM353620 VCaP_regular_medium_H3K4me3 20478527 ab8580 AbcamMACS 10.95 30043 GSM353624 VCaP_regular_medium_H3K35me3 20478527 ab9050Abcam SICER 9.91 29860 GSM353629 VCaP_regular_medium_Ace_H3 2047852706-599 Millipore MACS 4.76 41971 GSM353622 VCaP_regular_medium_Pan_H320478527 ab1791 Abcam MACS 5.91 control GSM353623VCaP_regular_medium_Polil 20478527 ab817 Abcam MACS 6.88 16041 GSM353634LNCaP_regular_medium_H3K4me1 20478527 ab8895 Abcam MACS 6.19 31109GSM353635 LNCaP_regular_medium_H3K4me2 20478527 ab7765 Abcam MACS 6.1462061 GSM353626 LNCaP_regular_medium_H3K4me3 20478527 ab8580 Abcam MACS10.22 19638 GSM353627 LNCaP_regular_medium_H3K36me3 20478527 ab9050Abcam SICER 9.15 24932 GSM353628 LNCaP_regular_medium_Ace_H3 2047852706-599 Millipore MACS 4.76 33211 GSM353617 LNCaP_Ethl_Polil 20478527ab817 Abcam MACS 1.36 8232 GSM353653 tissue_H3K4me3 20478527 ab8580Abcam MACS 11.85 23750

TABLE 4 Fold change SAM score Category Type Name Interval (Unlogged)((r)/(s + s0)) PROTEIN UPREG. TU_0084471_0 chr5: 33980375-34087770 12.757.71 NOVEL UPREG. TU_0099865_0 chr8: 128087842-128095202 7.07 7.41PROTEIN UPREG. TU_0123088_0 chr2: 238147710-238169707 3.01 7.01 ncRNAUPREG. TU_0102832_0 chr9: 78569118-78593537 12.23 6.93 PROTEIN UPREG.TU_0078322_0 chr12: 32260254-32260805 4.52 6.82 ncRNA UPREG.TU_0101270_0 chr21: 41853044-41875166 9.82 6.79 PROTEIN UPREG.TU_0027326_0 chrX: 16874726-17077384 3.31 6.79 PROTEIN UPREG.TU_0092114_0 chr11: 60223535-60239968 7.48 6.65 PROTEIN UPREG.TU_0044448_0 chr13: 51509122-51537693 4.77 6.59 PROTEIN UPREG.TU_0023159_0 chr19: 40224450-40249318 3.69 6.56 PROTEIN UPREG.TU_0092116_0 chr11: 60238519-60239968 7.50 6.44 PROTEIN UPREG.TU_0123090_0 chr2: 238164428-238165452 3.57 6.24 ncRNA UPREG.TU_0046239_0 chr4: 1185645-1201937 5.19 6.22 PROTEIN UPREG. TU_0122750_0chr2: 231610299-231625861 4.56 6.14 PROTEIN UPREG. TU_0082723_0 chr12:120142512-120219979 3.26 6.13 PROTEIN UPREG. TU_0123089_0 chr2:238164428-238165452 4.22 6.12 PROTEIN UPREG. TU_0101111_0 chr21:36989329-37045253 4.04 6.04 PROTEIN UPREG. TU_0090152_0 chr11:4965638-4969515 6.38 5.99 PROTEIN UPREG. TU_0101113_0 chr21:36994126-37045253 3.76 5.98 PROTEIN UPREG. TU_0045026_0 chr13:94660907-94668260 3.68 5.97 ncRNA UPREG. TU_0101274_0 chr21:41869930-41870631 8.95 5.88 PROTEIN UPREG. TU_0046235_0 chr4:1181913-1189142 4.28 5.87 NOVEL UPREG. TU_0054603_0 chr16:82380933-82394836 7.25 5.84 PROTEIN UPREG. TU_0101308_0 chr21:42605257-42608791 4.97 5.83 PROTEIN UPREG. TU_0084137_0 chr5:13981150-13997615 3.91 5.80 PROTEIN UPREG. TU_0084127_0 chr5:13882635-13892514 4.95 5.79 PROTEIN UPREG. TU_0101119_0 chr21:37034016-37045253 3.56 5.78 PROTEIN UPREG. TU_0054919_0 chr16:88188842-88191143 3.46 5.75 PROTEIN UPREG. TU_0120963_0 chr2:172658361-172662549 27.56 5.66 PROTEIN UPREG. TU_0044977_0 chr13:94524392-94621526 3.64 5.64 PROTEIN UPREG. TU_0052614_0 chr16:20542057-20616514 6.65 5.63 NOVEL UPREG. TU_0084303_0 chr5:15899476-15955226 7.46 5.61 PROTEIN UPREG. TU_0060406_0 chr1:28134091-28158290 3.03 5.61 PROTEIN UPREG. TU_0060407_0 chr1:28155047-28170460 2.41 5.60 ncRNA UPREG. TU_0103252_0 chr9:96357168-96369978 5.00 5.58 PROTEIN UPREG. TU_0034719_0 chr14:73490756-73555773 2.51 5.57 PROTEIN UPREG. TU_0070457_0 chr20:2258975-2269890 6.49 5.56 NOVEL UPREG. TU_0114240_0 chr2:1534883-1538193 5.25 5.54 PROTEIN UPREG. TU_0087676_0 chr5:138643394-138648458 2.75 5.50 PROTEIN UPREG. TU_0084138_0 chr5:13976388-13981285 4.09 5.48 ncRNA UPREG. TU_0046237_0 chr4:1162036-1195088 4.29 5.47 ncRNA UPREG. TU_0060421_0 chr1:28157480-28158290 3.12 5.44 PROTEIN UPREG. TU_0061436_0 chr1:37954250-37957136 2.66 5.41 PROTEIN UPREG. TU_0044894_0 chr13:94470096-94752898 2.85 5.38 PROTEIN UPREG. TU_0034720_0 chr14:73486609-73503474 2.20 5.38 PROTEIN UPREG. TU_0090153_0 chr11:4969009-4970186 7.37 5.34 PROTEIN UPREG. TU_0061432_0 chr1:37954250-37958679 2.65 5.31 PROTEIN UPREG. TU_0090268_0 chr11:6659768-6661138 1.76 5.30 PROTEIN UPREG. TU_0084120_0 chr5:13743434-13864864 3.59 5.29 PROTEIN UPREG. TU_0045059_0 chr13:94638351-94639152 2.93 5.28 ncRNA UPREG. TU_0075807_0 chr10:101676895-101680049 2.61 5.27 PROTEIN UPREG. TU_0078285_0 chr12:32150992-32421799 3.02 5.26 PROTEIN UPREG. TU_0103019_0 chr9:87826642-87905011 2.77 5.22 PROTEIN UPREG. TU_0046244_0 chr4:1185645-1216291 3.81 5.21 PROTEIN UPREG. TU_0075664_0 chr10:98752046-98935267 4.15 5.20 PROTEIN UPREG. TU_0090949_0 chr11:24475021-25059245 3.50 5.19 NOVEL UPREG. TU_0099864_0 chr8:128094589-128103681 3.56 5.17 PROTEIN UPREG. TU_0030273_0 chrX:106690714-106735138 3.52 5.15 PROTEIN UPREG. TU_0090128_0 chr11:4656012-4675667 5.26 5.15 PROTEIN UPREG. TU_0017700_0 chr17:51183394-51209728 2.05 5.13 ncRNA UPREG. TU_0018760_0 chr17:71645643-71652049 6.41 5.08 PROTEIN UPREG. TU_0018765_0 chr17:71652262-71747927 5.18 5.06 ncRNA UPREG. TU_0114235_0 chr2:1521347-1608386 4.22 5.04 PROTEIN UPREG. TU_0084132_0 chr5:13964466-13969509 4.30 5.03 NOVEL UPREG. TU_0049368_0 chr4:106772318-106772770 3.40 5.03 PROTEIN UPREG. TU_0115204_0 chr2:27175274-27195587 2.37 4.99 PROTEIN UPREG. TU_0115205_0 chr2:27163593-27178264 2.49 4.98 PROTEIN UPREG. TU_0062449_0 chr1:46418568-46424753 1.95 4.96 PROTEIN UPREG. TU_0072027_0 chr20:35964872-36007156 3.91 4.95 ncRNA UPREG. TU_0086706_0 chr5:116818427-116835522 2.91 4.92 PROTEIN UPREG. TU_0084136_0 chr5:13972327-13976416 3.37 4.91 PROTEIN UPREG. TU_0042761_0 chr13:23200813-23363662 3.54 4.90 PROTEIN UPREG. TU_0114168_0 chr15:99658271-99847175 2.25 4.89 ncRNA UPREG. TU_0018764_0 chr17:71650143-71652049 6.28 4.86 PROTEIN UPREG. TU_0085832_0 chr5:76150810-76167055 3.84 4.86 NOVEL UPREG. TU_0090142_0 chr11:4748677-4760303 12.08 4.86 PROTEIN UPREG. TU_0103018_0 chr9:87745936-87851451 2.41 4.83 NOVEL UPREG. TU_0096472_0 chr11:133844590-133862924 6.85 4.82 PROTEIN UPREG. TU_0029229_0 chrX:70349443-70377690 2.34 4.81 NOVEL UPREG. TU_0084306_0 chr5:15896315-15947088 5.37 4.78 PROTEIN UPREG. TU_0024934_0 chr19:54352845-54407356 1.88 4.77 NOVEL UPREG. TU_0096473_0 chr11:133844590-133862995 6.96 4.76 ncRNA UPREG. TU_0101131_0 chr21:36994126-37041774 3.57 4.74 PROTEIN UPREG. TU_0008239_0 chr7:7362390-7537552 3.00 4.73 PROTEIN UPREG. TU_0000022_0 chr6:1567640-2190842 2.14 4.72 PROTEIN UPREG. TU_0065193_0 chr1:145122471-145183544 2.72 4.72 PROTEIN UPREG. TU_0061439_0 chr1:37954250-37971671 2.46 4.71 ncRNA UPREG. TU_0096470_0 chr11:133841573-133850753 6.44 4.70 PROTEIN UPREG. TU_0046219_0 chr4:993725-995193 3.90 4.69 NOVEL UPREG. TU_0078288_0 chr12:32393283-32405731 2.47 4.67 PROTEIN UPREG. TU_0101115_0 chr21:37000839-37005920 3.31 4.67 NOVEL UPREG. TU_0099884_0 chr8:128301493-128307576 2.65 4.66 PROTEIN UPREG. TU_0008489_0 chr7:23685881-23708938 1.70 4.64 PROTEIN UPREG. TU_0042767_0 chr13:23186666-23204319 4.82 4.64 PROTEIN UPREG. TU_0061430_0 chr1:37930752-37957012 2.30 4.64 PROTEIN UPREG. TU_0079451_0 chr12:52696814-52736068 3.77 4.64 PROTEIN UPREG. TU_0069545_0 chr1:226711356-226712534 2.36 4.63 PROTEIN UPREG. TU_0045837_0 chr13:113151239-113151444 3.73 4.61 PROTEIN UPREG. TU_0101138_0 chr21:36994126-37004010 3.54 4.61 PROTEIN UPREG. TU_0049362_0 chr4:106693102-106771686 3.06 4.58 PROTEIN UPREG. TU_0055044_0 chr16:88589437-88613428 2.23 4.55 PROTEIN UPREG. TU_0038605_0 chr3:52689830-52704651 1.54 4.55 ncRNA UPREG. TU_0062653_0 chr1:51756544-51799759 2.52 4.54 PROTEIN UPREG. TU_0080359_0 chr12:63512292-63558861 1.87 4.53 PROTEIN UPREG. TU_0012481_0 chr7:111155336-111217889 2.04 4.52 PROTEIN UPREG. TU_0076355_0 chr10:115970327-115995953 10.34 4.52 PROTEIN UPREG. TU_0099892_0 chr8:128817416-128822629 2.33 4.52 ncRNA UPREG. TU_0050484_0 chr1:28706931-28707187 2.53 4.51 PROTEIN UPREG. TU_0046232_0 chr4:1147069-1175181 2.75 4.50 PROTEIN UPREG. TU_0107858_0 chr22:40664589-40673116 2.27 4.50 PROTEIN UPREG. TU_0042794_0 chr13:23228589-23228839 3.47 4.49 PROTEIN UPREG. TU_0057850_0 chr1:1523259-1525373 2.80 4.48 PROTEIN UPREG. TU_0023156_0 chr19:40109515-40127909 2.56 4.48 PROTEIN UPREG. TU_0102821_0 chr9:78263916-78312152 2.98 4.48 PROTEIN UPREG. TU_0081659_0 chr12:108636297-108700791 2.90 4.47 PROTEIN UPREG. TU_0049370_0 chr4:106776991-106847697 2.15 4.47 PROTEIN UPREG. TU_0047672_0 chr4:41807710-41840313 2.51 4.47 PROTEIN UPREG. TU_0114959_0 chr2:24865860-24869912 1.68 4.46 PROTEIN UPREG. TU_0037043_0 chr3:13332730-13436812 1.77 4.46 PROTEIN UPREG. TU_0087443_0 chr5:135237637-135247034 4.09 4.46 PROTEIN UPREG. TU_0086635_0 chr5:114489075-114543909 2.02 4.43 PROTEIN UPREG. TU_0107859_0 chr22:40664589-40665721 2.38 4.42 NOVEL UPREG. TU_0106548_0 chr22:22209111-22212055 6.49 4.42 PROTEIN UPREG. TU_0067165_0 chr1:160797907-160845907 1.81 4.40 PROTEIN UPREG. TU_0020146_0 chr19:3728970-3737293 2.53 4.39 PROTEIN UPREG. TU_0107642_0 chr22:39046992-39047479 1.69 4.38 PROTEIN UPREG. TU_0016185_0 chr17:31415814-31422953 3.63 4.38 NOVEL UPREG. TU_0104717_0 chr9:130697833-130698832 2.79 4.36 PROTEIN UPREG. TU_0052105_0 chr16:4785874-4786488 2.99 4.36 PROTEIN UPREG. TU_0059663_0 chr1:21795295-21850886 1.99 4.35 PROTEIN UPREG. TU_0108030_0 chr22:43527117-43638770 1.74 4.34 PROTEIN UPREG. TU_0093781_0 chr11:67151991-67154057 2.48 4.33 PROTEIN UPREG. TU_0086924_0 chr5:126233852-126241807 2.89 4.32 PROTEIN UPREG. TU_0048191_0 chr4:72423780-72424347 2.93 4.32 PROTEIN UPREG. TU_0034727_0 chr14:73508223-73508442 2.29 4.32 PROTEIN UPREG. TU_0096297_0 chr11:128342286-128353900 1.84 4.31 PROTEIN UPREG. TU_0007829_0 chr7:3625233-4275129 4.39 4.30 PROTEIN UPREG. TU_0116252_0 chr2:47449810-47467636 1.93 4.30 PROTEIN UPREG. TU_0115216_0 chr2:27175274-27177799 2.02 4.27 PROTEIN UPREG. TU_0018409_0 chr17:65013419-65049811 2.02 4.26 PROTEIN UPREG. TU_0099847_0 chr8:126511614-126519830 2.75 4.25 PROTEIN UPREG. TU_0035152_0 chr14:81062791-81063412 2.22 4.25 PROTEIN UPREG. TU_0040936_0 chr3:155391785-155458293 2.10 4.25 PROTEIN UPREG. TU_0027558_0 chrX:23595491-23614436 1.66 4.25 PROTEIN UPREG. TU_0076460_0 chr10:121248954-121292235 1.66 4.24 PROTEIN UPREG. TU_0067170_0 chr1:160826739-160826994 2.10 4.23 PROTEIN UPREG. TU_0103050_0 chr9:89409681-89512477 2.30 4.23 PROTEIN UPREG. TU_0112868_0 chr15:77390455-77402242 1.55 4.23 PROTEIN UPREG. TU_0090960_0 chr11:25059388-25060757 3.35 4.23 PROTEIN UPREG. TU_0072165_0 chr20:40142077-40204030 4.69 4.22 PROTEIN UPREG. TU_0044687_0 chr13:74756644-74954891 2.04 4.21 ncRNA UPREG. TU_0096477_0 chr11:133879414-133850753 4.43 4.21 PROTEIN UPREG. TU_0093947_0 chr11:68208575-68215238 1.41 4.20 PROTEIN UPREG. TU_0103253_0 chr9:96405246-96442373 1.69 4.20 PROTEIN UPREG. TU_0091863_0 chr11:57008498-57039966 2.69 4.20 PROTEIN UPREG. TU_0106199_0 chr22:18308042-18314411 3.94 4.20 NOVEL UPREG. TU_0090140_0 chr11:4748163-4759145 6.33 4.20 PROTEIN UPREG. TU_0103051_0 chr9:89302442-89409890 2.37 4.19 NOVEL UPREG. TU_0078290_0 chr12:32394534-32410898 3.20 4.19 PROTEIN UPREG. TU_0029336_0 chrX:70669659-70712461 1.70 4.18 PROTEIN UPREG. TU_0092155_0 chr11:60871597-60886554 1.80 4.18 PROTEIN UPREG. TU_0095597_0 chr11:114549577-114880335 1.75 4.18 PROTEIN UPREG. TU_0082724_0 chr12:120230545-120274615 1.42 4.17 PROTEIN UPREG. TU_0079770_0 chr12:55040666-55042824 4.25 4.16 PROTEIN UPREG. TU_0000263_0 chr6:4060925-4080831 1.55 4.16 NOVEL UPREG. TU_0040394_0 chr3:133418632-133441282 3.46 4.16 PROTEIN UPREG. TU_0066594_0 chr1:154245443-154257363 1.40 4.15 PROTEIN UPREG. TU_0099852_0 chr8:126515081-126519830 2.81 4.15 PROTEIN UPREG. TU_0100363_0 chr8:144891741-144899598 2.24 4.14 PROTEIN UPREG. TU_0096461_0 chr11:133751095-133757235 2.10 4.13 ncRNA UPREG. TU_0044488_0 chr13:51641093-51641330 2.76 4.13 PROTEIN UPREG. TU_0048990_0 chr4:95592056-95804933 2.30 4.13 NOVEL UPREG. TU_0078293_0 chr12:32396393-32414822 2.90 4.13 PROTEIN UPREG. TU_0046201_0 chr4:991841-1010686 2.57 4.12 PROTEIN UPREG. TU_0091866_0 chr11:57008498-57010253 2.54 4.12 PROTEIN UPREG. TU_0011133_0 chr7:94378726-94759741 1.77 4.12 PROTEIN UPREG. TU_0122941_0 chr2:234410713-234427931 3.28 4.12 PROTEIN UPREG. TU_0084131_0 chr5:13929889-13953380 2.62 4.12 NOVEL UPREG. TU_0084142_0 chr5:14017046-14021379 3.59 4.11 PROTEIN UPREG. TU_0087955_0 chr5:140931645-140931865 2.00 4.10 PROTEIN UPREG. TU_0085953_0 chr5:79410392-79410908 3.35 4.10 PROTEIN UPREG. TU_0022288_0 chr19:18357973-18360121 2.75 4.09 PROTEIN UPREG. TU_0085951_0 chr5:79366959-79414885 3.01 4.09 PROTEIN UPREG. TU_0060849_0 chr1:32572021-32574435 1.81 4.09 PROTEIN UPREG. TU_0087441_0 chr5:134934290-134942617 2.74 4.09 PROTEIN UPREG. TU_0042725_0 chr13:23148223-23200531 4.96 4.09 PROTEIN UPREG. TU_0039018_0 chr3:66510805-66634168 1.69 4.08 PROTEIN UPREG. TU_0096299_0 chr11:128340164-128347506 1.70 4.07 PROTEIN UPREG. TU_0022290_0 chr19:18357973-18359195 2.64 4.07 PROTEIN UPREG. TU_0100684_0 chr8:146190487-146191030 1.89 4.06 PROTEIN UPREG. TU_0042974_0 chr13:26148671-26148967 2.81 4.06 NOVEL UPREG. TU_0084308_0 chr5:15938753-15949124 4.09 4.06 NOVEL UPREG. TU_0082746_0 chr12:120197102-120197416 4.97 4.06 PROTEIN UPREG. TU_0014355_0 chr17:2650561-2887730 1.92 4.05 PROTEIN UPREG. TU_0114110_0 chr15:99250537-99274351 2.01 4.05 PROTEIN UPREG. TU_0096341_0 chr11:129534843-129585464 1.64 4.04 PROTEIN UPREG. TU_0052083_0 chr16:4784094-4805339 2.71 4.04 NOVEL UPREG. TU_0078196_0 chr12:32394534-32405549 2.92 4.04 PROTEIN UPREG. TU_0084126_0 chr5:13892443-13903812 3.64 4.03 NOVEL UPREG. TU_0047312_0 chr4:39217669-39222163 3.83 4.02 PROTEIN UPREG. TU_0008287_0 chr7:8119340-8268973 1.65 4.02 PROTEIN UPREG. TU_0018937_0 chr17:73714011-73714967 1.61 4.01 PROTEIN UPREG. TU_0048995_0 chr4:95805027-95808417 2.47 4.00 PROTEIN UPREG. TU_0038694_0 chr3:53810226-53855769 2.03 3.99 ncRNA UPREG. TU_0046233_0 chr4:1202157-1232168 2.45 3.99 PROTEIN UPREG. TU_0019018_0 chr17:75372094-75381243 2.25 3.98 PROTEIN UPREG. TU_0042326_0 chr3:199123974-199125319 1.77 3.98 PROTEIN UPREG. TU_0099893_0 chr8:128817416-128819105 2.23 3.98 PROTEIN UPREG. TU_0012491_0 chr7:111304238-111362856 1.91 3.98 PROTEIN UPREG. TU_0112335_0 chr15:70816880-70864494 1.71 3.97 PROTEIN UPREG. TU_0047964_0 chr4:57020861-57038533 1.74 3.97 PROTEIN UPREG. TU_0052565_0 chr16:19362784-19409995 1.98 3.96 NOVEL UPREG. TU_0042717_0 chr13:23149908-23200198 4.95 3.96 PROTEIN UPREG. TU_0017374_0 chr17:43380086-43404182 1.53 3.96 PROTEIN UPREG. TU_0071058_0 chr20:20318209-20549154 2.02 3.96 PROTEIN UPREG. TU_0105741_0 chrY:6971017-6998339 2.20 3.95 PROTEIN UPREG. TU_0018995_0 chr17:74491566-74517485 1.64 3.94 PROTEIN UPREG. TU_0103055_0 chr9:89512509-8913285 1.92 3.93 PROTEIN UPREG. TU_0041139_0 chr3:171237964-171285906 1.91 3.93 PROTEIN UPREG. TU_0042325_0 chr3:199124975-199143480 1.74 3.93 PROTEIN UPREG. TU_0020688_0 chr19:8180084-8237335 1.60 3.93 PROTEIN UPREG. TU_0118314_0 chr2:99086923-99100654 1.78 3.92 PROTEIN UPREG. TU_0017875_0 chr17:54652767-54706896 2.33 3.92 PROTEIN UPREG. TU_0037277_0 chr3:24134438-24511318 1.75 3.92 PROTEIN UPREG. TU_0047593_0 chr4:40446539-40457235 1.90 3.91 PROTEIN UPREG. TU_0114108_0 chr15:99235494-99274389 2.00 3.91 ncRNA UPREG. TU_0024530_0 chr19:50889160-50909766 1.72 3.91 PROTEIN UPREG. TU_0008957_0 chr7:38308886-38325338 2.62 3.91 PROTEIN UPREG. TU_0043122_0 chr13:28981555-28989371 1.73 3.90 PROTEIN UPREG. TU_0076644_0 chr10:127398227-127398596 2.06 3.90 PROTEIN UPREG. TU_0045423_0 chr13:100053877-100125079 2.02 3.89 PROTEIN UPREG. TU_0045495_0 chr13:107720446-107737194 2.06 3.88 PROTEIN UPREG. TU_0076648_0 chr10:127412714-127442685 1.64 3.88 NOVEL UPREG. TU_0088857_0 chr5:172259171-172275517 1.69 3.87 NOVEL UPREG. TU_0044453_0 chr13:51505777-51524522 2.96 3.86 NOVEL UPREG. TU_0047330_0 chr4:39217641-39222163 3.43 3.86 PROTEIN UPREG. TU_0100838_0 chr21:30508275-30510244 2.43 3.86 NOVEL UPREG. TU_0106544_0 chr22:22210421-22220506 4.27 3.85 ncRNA UPREG. TU_0100275_0 chr8:144520506-144537551 2.11 3.85 PROTEIN UPREG. TU_0057466_0 chr18:72853744-72866791 1.58 3.84 PROTEIN UPREG. TU_0040010_0 chr3:126311839-126412928 2.16 3.84 PROTEIN UPREG. TU_0042800_0 chr13:23360816-23370548 2.73 3.84 PROTEIN UPREG. TU_0117501_0 chr2:74065748-74174193 1.71 3.83 PROTEIN UPREG. TU_0053389_0 chr16:45673980-45701001 2.66 3.83 PROTEIN UPREG. TU_0087944_0 chr5:140874777-140978925 1.47 3.83 PROTEIN UPREG. TU_0017393_0 chr17:43389397-43390300 1.90 3.82 PROTEIN UPREG. TU_0008919_0 chr7:38257158-38271020 1.93 3.82 PROTEIN UPREG. TU_0033383_0 chr14:50259793-50367616 1.51 3.82 PROTEIN UPREG. TU_0049911_0 chr4:139304784-139382952 2.48 3.82 PROTEIN UPREG. TU_0024366_0 chr19:50100808-50104487 1.86 3.82 PROTEIN UPREG. TU_0070109_0 chr1:243979271-244159914 1.56 3.81 PROTEIN UPREG. TU_0120975_0 chr2:182104631-182107832 1.86 3.80 NOVEL UPREG. TU_0044933_0 chr13:94755992-94760688 2.52 3.80 PROTEIN UPREG. TU_0103689_0 chr9:111019219-111122750 1.75 3.80 PROTEIN UPREG. TU_0096460_0 chr11:133734857-133786962 2.09 3.79 PROTEIN UPREG. TU_0071115_0 chr20:24934888-24986948 1.48 3.79 PROTEIN UPREG. TU_0093783_0 chr11:67153661-67153870 2.48 3.79 PROTEIN UPREG. TU_0047591_0 chr4:40457999-40506655 1.79 3.79 PROTEIN UPREG. TU_0112336_0 chr15:70830765-70838346 1.63 3.78 PROTEIN UPREG. TU_0066664_0 chr1:154481433-154485049 2.29 3.78 PROTEIN UPREG. TU_0018812_0 chr17:72119376-72151549 3.38 3.78 PROTEIN UPREG. TU_0110225_0 chr15:48510091-48912722 3.60 3.78 ncRNA UPREG. TU_0054545_0 chr16:79431010-79431852 10.26 3.78 PROTEIN UPREG. TU_0107643_0 chr22:39072466-39093168 1.36 3.78 PROTEIN UPREG. TU_0025230_0 chr19:55992773-56000199 1.86 3.78 PROTEIN UPREG. TU_0012480_0 chr7:111153704-111155311 1.81 3.77 PROTEIN UPREG. TU_0070821_0 chr20:8997167-9409281 1.64 3.77 PROTEIN UPREG. TU_0103873_0 chr9:115151636-115178163 1.52 3.77 PROTEIN UPREG. TU_0018813_0 chr17:72128611-72133119 3.56 3.76 NOVEL UPREG. TU_0112004_0 chr15:67644390-67650387 3.56 3.76 PROTEIN UPREG. TU_0043118_0 chr13:28981555-29067829 1.76 3.76 NOVEL UPREG. TU_0112003_0 chr15:67645590-67775246 3.12 3.76 NOVEL UPREG. TU_0060446_0 chr1:28438629-28450156 2.23 3.75 PROTEIN UPREG. TU_0122972_0 chr2:236068012-236482693 1.69 3.75 NOVEL UPREG. TU_0106545_0 chr22:22218478-22219162 3.99 3.74 PROTEIN UPREG. TU_0087283_0 chr5:133753241-133766074 1.85 3.74 ncRNA UPREG. TU_0025312_0 chr19:57059515-57145170 1.89 3.74 PROTEIN UPREG. TU_0079679_0 chr12:54760142-54783545 1.58 3.73 PROTEIN UPREG. TU_0074564_0 chr10:64241765-64246112 2.62 3.73 PROTEIN UPREG. TU_0106189_0 chr22:18235213-18328816 1.82 3.73 PROTEIN UPREG. TU_0078994_0 chr12:49412412-49428706 1.41 3.72 ncRNA UPREG. TU_0003229_0 chr6:41598975-41621874 2.05 3.72 PROTEIN UPREG. TU_0040937_0 chr3:155439710-155458293 1.96 3.72 PROTEIN UPREG. TU_0040093_0 chr3:128830731-128874336 1.87 3.72 NOVEL UPREG. TU_0106542_0 chr22:22211315-22220506 3.77 3.71 PROTEIN UPREG. TU_0019375_0 chr17:77608812-77616980 1.63 3.71 PROTEIN UPREG. TU_0042563_0 chr13:20264762-20334966 1.85 3.71 PROTEIN UPREG. TU_0103386_0 chr9:9905734-99110148 1.89 3.71 PROTEIN UPREG. TU_0030004_0 chrX:100534013-100534540 1.84 3.71 NOVEL UPREG. TU_0089906_0 chr11:1042845-1045705 2.94 3.71 NOVEL UPREG. TU_0089014_0 chr5:176014905-176015351 2.01 3.71 ncRNA UPREG. TU_0056173_0 chr18:22523074-22537627 3.31 3.70 PROTEIN UPREG. TU_0052880_0 chr16:28393117-28411069 1.48 3.70 PROTEIN UPREG. TU_0100355_0 chr8:144884230-144910177 2.00 3.69 PROTEIN UPREG. TU_0096216_0 chr11:125271293-125271517 2.08 3.69 PROTEIN UPREG. TU_0092161_0 chr11:60884289-60892364 1.99 3.68 PROTEIN UPREG. TU_0086926_0 chr5:126241953-126394149 2.27 3.68 NOVEL UPREG. TU_0088230_0 chr5:148864170-148864752 1.94 3.68 ncRNA UPREG. TU_0099940_0 chr8:129065546-129182684 1.61 3.68 PROTEIN UPREG. TU_0089017_0 chr5:176222085-176240501 10.21 3.67 PROTEIN UPREG. TU_0078586_0 chr12:46643629-46648944 1.47 3.67 PROTEIN UPREG. TU_0053467_0 chr16:51028455-51138080 2.19 3.67 PROTEIN UPREG. TU_0089452_0 chr5:179258704-179258997 1.62 3.67 PROTEIN UPREG. TU_0076329_0 chr10:115501382-115531028 2.60 3.67 PROTEIN UPREG. TU_0047688_0 chr4:42105164-42354144 1.68 3.67 PROTEIN UPREG. TU_0059142_0 chr1:16203274-16206548 12.41 3.67 PROTEIN UPREG. TU_0116906_0 chr2:63135968-63138462 2.81 3.66 PROTEIN UPREG. TU_0000154_0 chr6:3063923-3099152 1.53 3.66 PROTEIN UPREG. TU_0088782_0 chr5:170625426-170659593 1.78 3.66 NOVEL UPREG. TU_0089905_0 chr11:1042845-1045705 2.77 3.66 PROTEIN UPREG. TU_0101704_0 chr9:3265495-3516005 2.33 3.64 ncRNA UPREG. TU_0044897_0 chr13:94746488-94760688 2.17 3.64 PROTEIN UPREG. TU_0071059_0 chr20:20549245-20641260 2.39 3.64 ncRNA UPREG. TU_0046268_0 chr4:1199698-1211108 1.93 3.63 PROTEIN UPREG. TU_0071601_0 chr20:32827590-32828002 1.75 3.62 PROTEIN UPREG. TU_0100712_0 chr21:15258179-15359100 2.14 3.62 PROTEIN UPREG. TU_0092156_0 chr11:60885030-60893249 1.45 3.62 PROTEIN UPREG. TU_0091402_0 chr11:46255779-46299542 1.71 3.62 PROTEIN UPREG. TU_0039018_0 chr3:66376322-66514060 1.50 3.62 PROTEIN UPREG. TU_0100378_0 chr8:144899799-144900640 2.00 3.62 NOVEL UPREG. TU_0112025_0 chr15:67780574-67782345 3.42 3.62 PROTEIN UPREG. TU_0106031_0 chr22:16336630-16412806 2.01 3.62 PROTEIN UPREG. TU_0050785_0 chr4:174395360-174453821 2.36 3.61 PROTEIN UPREG. TU_0058834_0 chr1:11768665-11783670 1.50 3.61 PROTEIN UPREG. TU_0039496_0 chr3:106753939-106754201 1.99 3.61 ncRNA UPREG. TU_0098397_0 chr8:69379259-69406175 2.73 3.61 PROTEIN UPREG. TU_0017847_0 chr17:54188675-54413808 2.82 3.61 PROTEIN UPREG. TU_0108299_0 chr22:49267227-49270226 2.03 3.60 PROTEIN UPREG. TU_0076846_0 chr10:135042714-135056670 2.27 3.59 PROTEIN UPREG. TU_0096351_0 chr11:129611827-129689996 1.61 3.59 PROTEIN UPREG. TU_0019298_0 chr17:77242472-77300154 1.51 3.59 PROTEIN UPREG. TU_0057465_0 chr18:72830973-7297379 1.56 3.59 PROTEIN UPREG. TU_0013475_0 chr7:148137800-148212367 1.74 3.59 PROTEIN UPREG. TU_0001426_0 chr6:28655044-28662198 2.56 3.59 NOVEL UPREG. TU_0106541_0 chr22:22209111-22219162 4.02 3.58 PROTEIN UPREG. TU_0073803_0 chr10:19005554-19007053 1.94 3.58 PROTEIN UPREG. TU_0040100_0 chr3:129253916-129289610 1.39 3.58 PROTEIN UPREG. TU_0001431_0 chr6:28978594-28999755 1.33 3.58 PROTEIN UPREG. TU_0076643_0 chr10:127398227-127407663 1.73 3.57 PROTEIN UPREG. TU_0089137_0 chr5:176814485-176815986 1.93 3.57 PROTEIN UPREG. TU_0098700_0 chr8:82806988-82833618 1.76 3.57 PROTEIN UPREG. TU_0093785_0 chr11:67186209-67198838 3.74 3.57 NOVEL UPREG. TU_0056168_0 chr18:22477042-22477886 3.05 3.57 PROTEIN UPREG. TU_0067222_0 chr1:164063363-164147501 1.63 3.57 PROTEIN UPREG. TU_0052172_0 chr16:8799176-8799379 1.61 3.57 PROTEIN UPREG. TU_0008360_0 chr7:16652301-16712672 1.46 3.57 PROTEIN UPREG. TU_0035610_0 chr14:93580687-93582188 2.08 3.56 PROTEIN UPREG. TU_0000168_0 chr6:3100128-3102765 2.10 3.56 PROTEIN UPREG. TU_0039649_0 chr3:115160992-115164502 1.72 3.56 PROTEIN UPREG. TU_0052843_0 chr16:27143818-27187607 1.42 3.56 NOVEL UPREG. TU_0024950_0 chr19:54450100-54452968 2.11 3.55 PROTEIN UPREG. TU_0008504_0 chr7:24656812-24693891 1.99 3.55 PROTEIN UPREG. TU_0061102_0 chr1:35671678-35795597 1.44 3.55 PROTEIN UPREG. TU_0032890_0 chr14:36736878-36788106 2.36 3.55 ncRNA UPREG. TU_0046241_0 chr4:1158292-1167160 2.53 3.55 NOVEL UPREG. TU_0008499_0 chr7:24236191-24236455 5.44 3.54 PROTEIN UPREG. TU_0100172_0 chr8:142471307-142511866 1.78 3.54 NOVEL UPREG. TU_0086543_0 chr5:110311813-110312092 1.53 3.53 PROTEIN UPREG. TU_0072450_0 chr20:44619899-44747359 1.83 3.53 NOVEL UPREG. TU_0044931_0 chr13:94755980-94759335 2.15 3.53 PROTEIN UPREG. TU_0093950_0 chr11:68214746-68215218 1.49 3.53 PROTEIN UPREG. TU_0006239_0 chr6:138649313-138671427 2.22 3.53 PROTEIN UPREG. TU_0065894_0 chr1:150044684-150070988 1.54 3.52 PROTEIN UPREG. TU_0078675_0 chr12:47602047-47602939 1.58 3.52 PROTEIN UPREG. TU_0052150_0 chr16:8799176-8864674 1.42 3.52 NOVEL UPREG. TU_0112021_0 chr15:67762926-67783593 2.66 3.52 PROTEIN UPREG. TU_0041581_0 chr3:185450132-185459240 1.77 3.52 PROTEIN UPREG. TU_0017269_0 chr17:42127174-42189979 1.59 3.52 PROTEIN UPREG. TU_0103138_0 chr9:94055563-94056563 1.61 3.52 PROTEIN UPREG. TU_0078683_0 chr12:47603989-47604485 1.69 3.52 PROTEIN UPREG. TU_0099209_0 chr11:6453771-6453210 1.44 3.51 ncRNA UPREG. TU_0045193_0 chr13:97851959-97852689 1.98 3.51 PROTEIN UPREG. TU_0050499_0 chr4:156862572-156862939 1.82 3.51 PROTEIN UPREG. TU_0088025_0 chr5:142130134-142254088 1.89 3.51 PROTEIN UPREG. TU_0052554_0 chr16:19329285-19424714 1.78 3.51 PROTEIN UPREG. TU_0085653_0 chr5:70918890-70990273 2.39 3.51 PROTEIN UPREG. TU_0101238_0 chr21:41610494-41651888 1.89 3.50 PROTEIN UPREG. TU_0098689_0 chr8:82355436-82355977 4.15 3.49 PROTEIN UPREG. TU_0100271_0 chr8:144522379-144537551 1.93 3.49 PROTEIN UPREG. TU_0013258_0 chr7:139750340-139773086 1.85 3.49 PROTEIN UPREG. TU_0122559_0 chr2:224338108-224338327 2.32 3.49 PROTEIN UPREG. TU_0068947_0 chr1:212567070-212567723 1.74 3.48 PROTEIN UPREG. TU_0101300_0 chr21:42512421-42593934 1.60 3.48 PROTEIN UPREG. TU_0105268_0 chr9:138238011-138277254 1.49 3.47 PROTEIN UPREG. TU_0080269_0 chr12:62524730-62664317 2.05 3.47 PROTEIN UPREG. TU_0001992_0 chr6:31939105-31955076 1.56 3.47 PROTEIN UPREG. TU_0018485_0 chr17:70458432-70480451 1.58 3.47 ncRNA UPREG. TU_0050493_0 chr1:28705947-28706605 1.60 2.46 PROTEIN UPREG. TU_0085975_0 chr5:79478814-79495113 1.91 3.46 PROTEIN UPREG. TU_0018919_0 chr17:73678343-73714970 1.48 3.46 ncRNA UPREG. TU_0054534_0 chr16:79404014-79431652 9.85 3.46 PROTEIN UPREG. TU_0076107_0 chr10:104454315-104488075 1.67 3.45 ncRNA UPREG. TU_0069658_0 chr1:229724782-229731269 1.75 3.45 NOVEL UPREG. TU_0120387_0 chr2:170267824-170281386 2.10 3.45 PROTEIN UPREG. TU_0015665_0 chr17:24073407-24077926 1.52 3.45 ncRNA UPREG. TU_0070414_0 chr20:1254059-1303172 1.68 3.45 NOVEL UPREG. TU_0072624_0 chr20:47335522-47338977 1.65 3.45 PROTEIN UPREG. TU_0012495_0 chr7:111373031-111411626 2.29 3.45 PROTEIN UPREG. TU_0076659_0 chr10:127514501-127526128 1.31 3.45 PROTEIN UPREG. TU_0088525_0 chr5:156625701-156755178 1.53 3.45 PROTEIN UPREG. TU_0046096_0 chr4:759449-809939 2.01 3.44 ncRNA UPREG. TU_0074332_0 chr10:43420869-43421283 1.52 3.44 PROTEIN UPREG. TU_0082983_0 chr12:121778239-121779189 2.65 3.44 PROTEIN UPREG. TU_0008361_0 chr7:16759923-16790805 1.58 3.44 PROTEIN UPREG. TU_0061443_0 chr1:38032067-38039550 1.67 3.44 PROTEIN UPREG. TU_0042715_0 chr13:23148223-23204319 3.68 3.43 ncRNA UPREG. TU_0119128_0 chr2:118310197-118313068 1.62 3.43 PROTEIN UPREG. TU_0112349_0 chr15:70834440-70835126 1.67 3.43 PROTEIN UPREG. TU_0027543_0 chrX:21921233-21922374 2.48 3.43 PROTEIN UPREG. TU_0062582_0 chr1:47489058-47552320 1.83 3.43 ncRNA UPREG. TU_0050791_0 chr4:174322695-174323924 2.13 3.41 PROTEIN UPREG. TU_0048346_0 chr4:77175264-77176185 2.48 3.41 NOVEL UPREG. TU_0093068_0 chr11:64956616-64961189 2.13 3.41 PROTEIN UPREG. TU_0033869_0 chr14:60248258-60260801 1.21 3.41 PROTEIN UPREG. TU_0000031_0 chr6:2190031-2190908 2.44 3.41 PROTEIN UPREG. TU_0082131_0 chr12:111151572-111152227 1.88 3.40 PROTEIN UPREG. TU_0038169_0 chr3:49035494-49041923 1.35 3.40 NOVEL UPREG. TU_0044898_0 chr13:94753009-94760688 2.11 3.40 PROTEIN UPREG. TU_0089144_0 chr5:176814489-176815986 1.86 3.40 PROTEIN UPREG. TU_0094504_0 chr11:74812477-74817273 2.40 3.40 PROTEIN UPREG. TU_0035633_0 chr14:94304291-94305127 2.17 3.40 PROTEIN UPREG. TU_0085819_0 chr5:75734806-76039614 1.64 3.40 PROTEIN UPREG. TU_0061431_0 chr1:37961347-37973585 2.62 3.40 NOVEL UPREG. TU_0078299_0 chr12:32290896-32292169 3.67 3.39 PROTEIN UPREG. TU_0004059_0 chr6:52976378-53034598 1.65 3.39 PROTEIN UPREG. TU_0098927_0 chr8:95722432-95788870 1.48 3.39 ncRNA UPREG. TU_0013886_0 chr7:155957953-156090820 2.50 3.39 PROTEIN UPREG. TU_0068377_0 chr1:201452418-201458956 1.84 3.39 NOVEL UPREG. TU_0101035_0 chr21:35419563-36421930 1.84 3.39 PROTEIN UPREG. TU_0062957_0 chr1:54089897-54128073 1.43 3.39 PROTEIN UPREG. TU_0099854_0 chr8:127633901-127639897 1.65 3.38 PROTEIN UPREG. TU_0048743_0 chr4:87924751-87955166 1.47 3.38 PROTEIN UPREG. TU_0086478_0 chr5:102510255-102521832 1.95 3.38 PROTEIN UPREG. TU_0120565_0 chr2:172672776-172675279 4.31 3.38 PROTEIN UPREG. TU_0122360_0 chr2:219554051-219557439 2.92 3.38 PROTEIN UPREG. TU_0092154_0 chr11:60857271-60874474 1.44 3.37 PROTEIN UPREG. TU_0015718_0 chr17:24095069-24100305 1.64 3.37 PROTEIN UPREG. TU_0039284_0 chr3:95208586-95249573 2.23 3.37 PROTEIN UPREG. TU_0082089_0 chr12:111082307-111187476 1.44 3.37 PROTEIN UPREG. TU_0035148_0 chr14:81009021-81069951 1.64 3.37 PROTEIN UPREG. TU_0054849_0 chr16:87403253-87406669 1.47 3.37 PROTEIN UPREG. TU_0113376_0 chr15:87432680-87545107 2.13 3.36 PROTEIN UPREG. TU_0019481_0 chr17:77998514-77999441 1.55 3.36 PROTEIN UPREG. TU_0007004_0 chr6:158396021-158440190 1.47 3.36 PROTEIN UPREG. TU_0092190_0 chr11:60876795-60877493 1.85 3.36 ncRNA UPREG. TU_0001996_0 chr6:31941546-31959679 1.43 3.36 NOVEL UPREG. TU_0066689_0 chr1:154509233-154510967 1.61 3.36 PROTEIN UPREG. TU_0035151_0 chr14:81015445-81021875 2.00 3.35 PROTEIN UPREG. TU_0092866_0 chr11:63975211-63975675 3.20 3.35 PROTEIN UPREG. TU_0050482_0 chr4:156807332-156877628 1.69 3.35 PROTEIN UPREG. TU_0022391_0 chr19:19076718-19094443 1.60 3.35 PROTEIN UPREG. TU_0048729_0 chr4:87734463-87924734 1.74 3.35 PROTEIN UPREG. TU_0103472_0 chr9:100534124-100570357 1.61 3.35 PROTEIN UPREG. TU_0087465_0 chr5:136431191-136431490 2.47 3.35 PROTEIN UPREG. TU_0058833_0 chr1:11768665-11788581 1.45 3.34 PROTEIN DOWNREG. TU_0009047_0 chr7:41967123-41970103 0.65 −3.35 PROTEIN DOWNREG. TU_0020039_0 chr19:2948637-2980244 0.65 −3.36 PROTEIN DOWNREG. TU_0024046_0 chr19:47194316-47201741 0.53 −3.36 PROTEIN DOWNREG. TU_0120035_0 chr2:154042114-154043553 0.49 −3.36 PROTEIN DOWNREG. TU_0014542_0 chr17:4790024-4790984 0.77 −3.36 PROTEIN DOWNREG. TU_0058703_0 chr1:10457547-10613394 0.66 −3.37 NOVEL DOWNREG. TU_0084922_0 chr5:44337219-44338127 0.51 −3.37 PROTEIN DOWNREG. TU_0067333_0 chr1:167362572-167539064 0.68 −3.37 PROTEIN DOWNREG. TU_0030086_0 chrX:101794939-101798995 0.64 −3.37 PROTEIN DOWNREG. TU_0031101_0 chrX:134247418-134254372 0.69 −3.37 PROTEIN DOWNREG. TU_0063762_0 chr1:87566944-87583813 0.66 −3.38 PROTEIN DOWNREG. TU_0107584_0 chr22:38075931-38123808 0.66 −3.38 PROTEIN DOWNREG. TU_0102296_0 chr9:34979701-34988409 0.57 −3.38 PROTEIN DOWNREG. TU_0038455_0 chr3:51951847-51958668 0.65 −3.38 PROTEIN DOWNREG. TU_0062948_0 chr1:53744574-53746867 0.46 −3.38 PROTEIN DOWNREG. TU_0092655_0 chr11:63282470-63288729 0.73 −3.38 PROTEIN DOWNREG. TU_0035606_0 chr14:93470258-93500717 0.58 −3.38 PROTEIN DOWNREG. TU_0055588_0 chr18:10470831-10478699 0.58 −3.38 PROTEIN DOWNREG. TU_0056462_0 chr18:41558112-41584622 0.49 −3.39 PROTEIN DOWNREG. TU_0002739_0 chr6:35321958-35328561 0.55 −3.39 PROTEIN DOWNREG. TU_0030147_0 chrX:102727067-102729284 0.65 −3.39 NOVEL DOWNREG. TU_0030209_0 chrX:103250901-103253228 0.66 −3.39 ncRNA DOWNREG. TU_0068206_0 chr1:200132176-200134973 0.60 −3.39 PROTEIN DOWNREG. TU_0081627_0 chr12:108186419-108190411 0.63 −3.40 PROTEIN DOWNREG. TU_0068194_0 chr1:200132176-200182322 0.59 −3.40 PROTEIN DOWNREG. TU_0049308_0 chr4:104220026-104220361 0.46 −3.40 NOVEL DOWNREG. TU_0068431_0 chr1:202350966-202363482 0.62 −3.40 PROTEIN DOWNREG. TU_0073506_0 chr10:7630096-7723984 0.60 −3.40 PROTEIN DOWNREG. TU_0054695_0 chr16:83411105-83499914 0.62 −3.40 PROTEIN DOWNREG. TU_0012556_0 chr7:115934290-115935899 0.50 −3.41 PROTEIN DOWNREG. TU_0018647_0 chr17:71259157-71294839 0.74 −3.41 NOVEL DOWNREG. TU_0030577_0 chrX:118036531-118036860 0.43 −3.41 PROTEIN DOWNREG. TU_0089961_0 chr11:2248339-2247566 0.52 −3.41 PROTEIN DOWNREG. TU_0000888_0 chr6:19947236-19950403 0.56 −3.41 PROTEIN DOWNREG. TU_0002212_0 chr6:32224073-32226328 0.56 −3.41 PROTEIN DOWNREG. TU_0024749_0 chr19:52937559-52939100 0.58 −3.41 PROTEIN DOWNREG. TU_0101225_0 chr21:40161189-40161418 0.52 −3.41 ncRNA DOWNREG. TU_0100030_0 chr8:134653589-134655310 0.41 −3.41 PROTEIN DOWNREG. TU_0102256_0 chr9:34356684-34366854 0.56 −3.41 PROTEIN DOWNREG. TU_0039040_0 chr3:69107066-69108860 0.62 −3.42 ncRNA DOWNREG. TU_0115808_0 chr2:37722515-37725828 0.61 −3.42 PROTEIN DOWNREG. TU_0115807_0 chr2:37722515-37725828 0.61 −3.42 NOVEL DOWNREG. TU_0038811_0 chr3:57890130-57890834 0.43 −3.43 PROTEIN DOWNREG. TU_0107000_0 chr22:29790122-29830660 0.60 −3.43 PROTEIN DOWNREG. TU_0065126_0 chr1:144274405-144279906 0.53 −3.43 PROTEIN DOWNREG. TU_0065093_0 chr1:144167535-144181746 0.72 −3.43 PROTEIN DOWNREG. TU_0066887_0 chr1:158352167-158379985 0.56 −3.44 PROTEIN DOWNREG. TU_0034681_0 chr14:73248261-73250867 0.61 −3.44 PROTEIN DOWNREG. TU_0064872_0 chr1:115373945-115394701 0.60 −3.44 PROTEIN DOWNREG. TU_0115146_0 chr2:26806070-26809827 0.49 −3.44 PROTEIN DOWNREG. TU_0023552_0 chr19:43433715-43439100 0.52 −3.44 PROTEIN DOWNREG. TU_0013056_0 chr2:134269121-134269574 0.41 −3.44 PROTEIN DOWNREG. TU_0078015_0 chr12:21809160-21817495 0.61 −3.45 PROTEIN DOWNREG. TU_0010849_0 chr7:84462824-84464278 0.41 −3.45 PROTEIN DOWNREG. TU_0018278_0 chr17:62235564-62237319 0.62 −3.45 PROTEIN DOWNREG. TU_0106896_0 chr22:28206216-28217370 0.46 −3.46 PROTEIN DOWNREG. TU_0086308_0 chr5:95158335-95154222 0.54 −3.46 PROTEIN DOWNREG. TU_0059500_0 chr1:19842799-19857540 0.66 −3.46 PROTEIN DOWNREG. TU_0030156_0 chrX:102749504-102752161 0.61 −3.46 PROTEIN DOWNREG. TU_0053209_0 chr16:30815439-30839057 0.45 −3.46 PROTEIN DOWNREG. TU_0102372_0 chr9:35672000-35681106 0.58 −3.46 PROTEIN DOWNREG. TU_0040491_0 chr3:134947802-134980329 0.35 −3.46 PROTEIN DOWNREG. TU_0063025_0 chr1:54832256-54849445 0.56 −3.46 PROTEIN DOWNREG. TU_0016741_0 chr17:37808007-37818100 0.61 −3.47 PROTEIN DOWNREG. TU_0079872_0 chr12:53272841-55276238 0.70 −3.47 NOVEL DOWNREG. TU_0072214_0 chr20:42166331-42172501 0.45 −3.47 PROTEIN DOWNREG. TU_0069254_0 chr1:223745864-223750945 0.54 −3.48 PROTEIN DOWNREG. TU_0014474_0 chr17:4410320-4410614 0.34 −3.48 PROTEIN DOWNREG. TU_0002034_0 chr6:31975375-31977685 0.61 −3.48 ncRNA DOWNREG. TU_0115805_0 chr2:37722515-37727509 0.64 −3.48 PROTEIN DOWNREG. TU_0106487_0 chr22:21742726-21797216 0.56 −3.48 PROTEIN DOWNREG. TU_0100880_0 chr21:32808766-32809639 0.62 −3.48 PROTEIN DOWNREG. TU_0028960_0 chrX:64873768-64873981 0.59 −3.48 PROTEIN DOWNREG. TU_0103717_0 chr9:112675334-112676369 0.59 −3.48 PROTEIN DOWNREG. TU_0016732_0 chr17:37807991-37828819 0.65 −3.48 PROTEIN DOWNREG. TU_0075573_0 chr10:96987317-97040810 0.65 −3.48 PROTEIN DOWNREG. TU_0108979_0 chr15:34659121-34889737 0.68 −3.48 PROTEIN DOWNREG. TU_0039868_0 chr3:123526763-123543198 0.51 −3.48 PROTEIN DOWNREG. TU_0032236_0 chr14:22885061-22893832 0.61 −3.48 PROTEIN DOWNREG. TU_0103902_0 chr9:115957988-116128421 0.59 −3.49 PROTEIN DOWNREG. TU_0004251_0 chr6:71069214-71069482 0.36 −3.49 PROTEIN DOWNREG. TU_0115344_0 chr2:27568254-27571592 0.64 −3.49 NOVEL DOWNREG. TU_0094307_0 chr11:7977293-7979927 0.69 −3.49 NOVEL DOWNREG. TU_0020914_0 chr19:9718612-9721799 0.47 −3.49 PROTEIN DOWNREG. TU_0014009_0 chr7:158513133-158630217 0.48 −3.50 PROTEIN DOWNREG. TU_0111467_0 chr15:62817064-62854842 0.58 −3.50 NOVEL DOWNREG. TU_0088552_0 chr5:157103352-157120455 0.64 −3.50 PROTEIN DOWNREG. TU_0016616_0 chr17:36992038-37034423 0.44 −3.50 PROTEIN DOWNREG. TU_0109820_0 chr15:41600571-41611159 0.56 −3.51 PROTEIN DOWNREG. TU_0083744_0 chr5:236838-237985 0.50 −3.51 PROTEIN DOWNREG. TU_0038899_0 chr3:58465926-58495812 0.58 −3.51 PROTEIN DOWNREG. TU_0018817_0 chr17:72183287-72184800 0.61 −3.51 PROTEIN DOWNREG. TU_0096362_0 chr11:129779777-129794214 0.56 −3.51 ncRNA DOWNREG. TU_0104765_0 chr9:131134480-131144297 0.53 −3.51 PROTEIN DOWNREG. TU_0047809_0 chr4:52581019-52582331 0.62 −3.52 PROTEIN DOWNREG. TU_0114638_0 chr2:11804193-11884972 0.68 −3.52 PROTEIN DOWNREG. TU_0110215_0 chr15:43246574-43254766 0.63 −3.52 PROTEIN DOWNREG. TU_0117024_0 chr2:66515747-66653430 0.61 −3.52 PROTEIN DOWNREG. TU_0109004_0 chr15:35178588-35180010 0.39 −3.53 PROTEIN DOWNREG. TU_0114005_0 chr15:97462760-97493368 0.56 −3.53 PROTEIN DOWNREG. TU_0079534_0 chr12:53260191-53268540 0.41 −3.53 PROTEIN DOWNREG. TU_0058435_0 chr1:202366748-202385528 0.62 −3.53 PROTEIN DOWNREG. TU_0014730_0 chr17:7034460-7061662 0.61 −3.53 PROTEIN DOWNREG. TU_0111099_0 chr15:57738640-57756015 0.70 −3.54 PROTEIN DOWNREG. TU_0079355_0 chr12:51906937-51912605 0.54 −3.54 PROTEIN DOWNREG. TU_0107389_0 chr22:36670710-36671784 0.59 −3.54 PROTEIN DOWNREG. TU_0105434_0 chr9:138991774-138996018 0.54 −3.54 ncRNA DOWNREG. TU_0122441_0 chr2:220000172-220002664 0.38 −3.54 PROTEIN DOWNREG. TU_0074041_0 chr10:29785041-30065975 0.64 −3.55 PROTEIN DOWNREG. TU_0114819_0 chr2:23779564-23785016 0.65 −3.55 PROTEIN DOWNREG. TU_0013666_0 chr7:150180552-150189309 0.34 −3.55 PROTEIN DOWNREG. TU_0036844_0 chr3:9930678-9933062 0.54 −3.56 PROTEIN DOWNREG. TU_0014467_0 chr17:4407802-4410614 0.49 −3.56 NOVEL DOWNREG. TU_0036397_0 chr14:104617328-104624500 0.45 −3.56 PROTEIN DOWNREG. TU_0014721_0 chr17:6882853-6884238 0.60 −3.57 PROTEIN DOWNREG. TU_0061867_0 chr1:41618433-41621890 0.61 −3.57 PROTEIN DOWNREG. TU_0090901_0 chr11:20061238-20099725 0.60 −3.57 PROTEIN DOWNREG. TU_0089503_0 chr5:179949721-179951068 0.47 −3.57 NOVEL DOWNREG. TU_0112056_0 chr15:69658838-69678469 0.46 −3.57 NOVEL DOWNREG. TU_0052454_0 chr16:15702084-15702374 0.40 −3.57 PROTEIN DOWNREG. TU_0004248_0 chr6:70983350-71069482 0.52 −3.57 PROTEIN DOWNREG. TU_0111118_0 chr15:58426685-58428608 0.59 −3.58 PROTEIN DOWNREG. TU_0047256_0 chr4:38781223-38804739 0.63 −3.58 PROTEIN DOWNREG. TU_0092308_0 chr11:61395022-61326508 0.62 −3.58 PROTEIN DOWNREG. TU_0037381_0 chr3:33159367-33165995 0.70 −3.59 PROTEIN DOWNREG. TU_0088765_0 chr5:169737435-169749043 0.53 −3.60 PROTEIN DOWNREG. TU_0039072_0 chr3:70098064-70100160 0.63 −3.60 NOVEL DOWNREG. TU_0112059_0 chr15:69667695-69691724 0.41 −3.60 PROTEIN DOWNREG. TU_0030975_0 chrX:130235170-130235814 0.49 −3.60 PROTEIN DOWNREG. TU_0038532_0 chr3:52258212-52287726 0.77 −3.60 PROTEIN DOWNREG. TU_0014418_0 chr17:3748115-3749717 0.39 −3.60 PROTEIN DOWNREG. TU_0001986_0 chr6:31791087-31793378 0.48 −3.61 PROTEIN DOWNREG. TU_0111109_0 chr15:58426685-58477514 0.66 −3.61 PROTEIN DOWNREG. TU_0064151_0 chr1:98933515-98937074 0.46 −3.61 PROTEIN DOWNREG. TU_0111253_0 chr15:61121812-61151157 0.63 −3.61 PROTEIN DOWNREG. TU_0058947_0 chr1:13782811-13817026 0.61 −3.62 PROTEIN DOWNREG. TU_0031484_0 chrX:151890690-151892673 0.59 −3.62 PROTEIN DOWNREG. TU_0076212_0 chr10:105781059-105835687 0.47 −3.62 PROTEIN DOWNREG. TU_0062567_0 chr1:47050692-47056967 0.47 −3.62 NOVEL DOWNREG. TU_0020667_0 chr19:7888598-7889980 0.41 −3.62 PROTEIN DOWNREG. TU_0029358_0 chrX:71263703-71268507 0.66 −3.63 PROTEIN DOWNREG. TU_0065339_0 chr1:148457403-148475104 0.56 −3.63 PROTEIN DOWNREG. TU_0063765_0 chr1:87583567-87587269 0.58 −3.63 NOVEL DOWNREG. TU_0036395_0 chr14:104617328-104623671 0.53 −3.63 PROTEIN DOWNREG. TU_0103872_0 chr9:115178483-115203441 0.59 −3.63 PROTEIN DOWNREG. TU_0050244_0 chr4:148665059-148685558 0.63 −3.63 PROTEIN DOWNREG. TU_0031913_0 chr14:20554755-20563715 0.64 −3.63 PROTEIN DOWNREG. TU_0065343_0 chr1:148501147-148501585 0.37 −3.63 PROTEIN DOWNREG. TU_0084946_0 chr5:50715235-50726033 0.60 −3.64 PROTEIN DOWNREG. TU_0090342_0 chr11:8671475-8849482 0.64 −3.64 PROTEIN DOWNREG. TU_0120044_0 chr2:155422693-155423038 0.26 −3.64 PROTEIN DOWNREG. TU_0023267_0 chr19:40937280-40940189 0.52 −3.64 PROTEIN DOWNREG. TU_0023553_0 chr19:43433715-43434071 0.51 −3.65 PROTEIN DOWNREG. TU_0115806_0 chr2:37722515-37725663 0.60 −3.65 PROTEIN DOWNREG. TU_0085256_0 chr5:59099679-59100724 0.53 −3.65 PROTEIN DOWNREG. TU_0038056_0 chr3:48563574-48623119 0.68 −3.65 PROTEIN DOWNREG. TU_0022088_0 chr19:16864768-16929718 0.55 −3.65 ncRNA DOWNREG. TU_0083408_0 chr12:129197899-129212499 0.58 −3.65 PROTEIN DOWNREG. TU_0059155_0 chr1:16397144-16405288 0.61 −3.65 PROTEIN DOWNREG. TU_0046595_0 chr4:3264594-3411502 0.68 −3.65 PROTEIN DOWNREG. TU_0099476_0 chr8:108331106-108578694 0.58 −3.66 PROTEIN DOWNREG. TU_0091498_0 chr11:46834081-46849744 0.65 −3.66 PROTEIN DOWNREG. TU_0098389_0 chr8:68586418-68699042 0.45 −3.66 PROTEIN DOWNREG. TU_0046627_0 chr4:3735533-3740037 0.45 −3.67 NOVEL DOWNREG. TU_0103946_0 chr9:116821701-116822181 0.48 −3.67 PROTEIN DOWNREG. TU_0008057_0 chr7:5519816-5536775 0.62 −3.67 PROTEIN DOWNREG. TU_0100219_0 chr8:143849604-143856276 0.59 −3.67 PROTEIN DOWNREG. TU_0087532_0 chr5:137802544-137810548 0.53 −3.68 PROTEIN DOWNREG. TU_0066743_0 chr1:154859563-154862200 0.43 −3.68 PROTEIN DOWNREG. TU_0052586_0 chr16:19637116-19779369 0.64 −3.68 PROTEIN DOWNREG. TU_0075808_0 chr10:88708340-88712998 0.51 −3.68 PROTEIN DOWNREG. TU_0032240_0 chr14:22894093-22905632 0.57 −3.68 PROTEIN DOWNREG. TU_0046399_0 chr4:2031053-2040569 0.44 −3.70 PROTEIN DOWNREG. TU_0081487_0 chr12:104248577-104289423 0.56 −3.70 PROTEIN DOWNREG. TU_0096978_0 chr8:22133174-22140355 0.47 −3.70 PROTEIN DOWNREG. TU_0054692_0 chr16:83411105-83500616 0.62 −3.70 PROTEIN DOWNREG. TU_0067818_0 chr1:180809414-180811333 0.72 −3.71 PROTEIN DOWNREG. TU_0098841_0 chr8:92038228-92039575 0.39 −3.71 PROTEIN DOWNREG. TU_0121595_0 chr2:202193170-202196672 0.62 −3.71 PROTEIN DOWNREG. TU_0023218_0 chr19:40679964-40694184 0.55 −3.71 PROTEIN DOWNREG. TU_0112386_0 chr15:71818130-71820041 0.55 −3.71 PROTEIN DOWNREG. TU_0024601_0 chr19:51605296-51609005 0.56 −3.71 PROTEIN DOWNREG. TU_0055238_0 chr18:2561572-2606627 0.59 −3.71 PROTEIN DOWNREG. TU_0085908_0 chr5:78401241-78420780 0.52 −3.72 ncRNA DOWNREG. TU_0111315_0 chr15:61676589-61681634 0.55 −3.72 PROTEIN DOWNREG. TU_0111311_0 chr15:61676589-61681634 0.55 −3.72 PROTEIN DOWNREG. TU_0023241_0 chr19:40856254-40861198 0.41 −3.72 PROTEIN DOWNREG. TU_0068139_0 chr1:199127296-199147465 0.42 −3.72 ncRNA DOWNREG. TU_0102684_0 chr9:70336502-70344481 0.56 −3.73 PROTEIN DOWNREG. TU_0068764_0 chr1:207854842-207892483 0.49 −3.73 PROTEIN DOWNREG. TU_0053636_0 chr16:55846971-55853340 0.58 −3.74 PROTEIN DOWNREG. TU_0084025_0 chr5:6501949-6545706 0.54 −3.74 NOVEL DOWNREG. TU_0032151_0 chr14:22508055-22508830 0.58 −3.74 PROTEIN DOWNREG. TU_0014680_0 chr17:6295379-6305574 0.62 −3.74 PROTEIN DOWNREG. TU_0076124_0 chr10:104619299-104651033 0.60 −3.75 PROTEIN DOWNREG. TU_0085198_0 chr5:58300638-58305429 0.60 −3.75 PROTEIN DOWNREG. TU_0102686_0 chr9:70337677-70344573 0.55 −3.76 PROTEIN DOWNREG. TU_0112385_0 chr15:71818130-71831566 0.54 −3.76 PROTEIN DOWNREG. TU_0100875_0 chr21:32705500-32809639 0.61 −3.78 PROTEIN DOWNREG. TU_0065928_0 chr1:151800274-151855449 0.49 −3.78 PROTEIN DOWNREG. TU_0063298_0 chr1:62474433-62474872 0.36 −3.78 PROTEIN DOWNREG. TU_0100851_0 chr21:32604246-32608457 0.62 −3.79 PROTEIN DOWNREG. TU_0101015_0 chr21:35010830-35012376 0.55 −3.79 ncRNA DOWNREG. TU_0031086_0 chrX:133993992-133995935 0.73 −3.79 PROTEIN DOWNREG. TU_0068759_0 chr1:207669209-207672813 0.45 −3.79 NOVEL DOWNREG. TU_0069253_0 chr1:223741202-223745600 0.62 −3.79 PROTEIN DOWNREG. TU_0020150_0 chr19:3877291-3879097 0.52 −3.79 ncRNA DOWNREG. TU_0084069_0 chr5:9599340-9603383 0.50 −3.80 PROTEIN DOWNREG. TU_0016922_0 chr17:38430856-38435173 0.51 −3.80 PROTEIN DOWNREG. TU_0013053_0 chr7:134114695-134305949 0.56 −3.81 PROTEIN DOWNREG. TU_0017406_0 chr17:43458534-43470076 0.58 −3.81 PROTEIN DOWNREG. TU_0014681_0 chr17:6295379-6305877 0.50 −3.81 PROTEIN DOWNREG. TU_0058447_0 chr1:9040090-9052233 0.36 −3.81 PROTEIN DOWNREG. TU_0055624_0 chr18:11872611-11875972 0.64 −3.82 PROTEIN DOWNREG. TU_0003717_0 chr6:43381215-43381963 0.49 −3.82 NOVEL DOWNREG. TU_0016578_0 chr17:35881203-35884855 0.52 −3.82 PROTEIN DOWNREG. TU_0101224_0 chr21:40161189-40223184 0.50 −3.82 PROTEIN DOWNREG. TU_0064871_0 chr1:115391459-115433611 0.59 −3.83 PROTEIN DOWNREG. TU_0097462_0 chr8:37773618-37822041 0.55 −3.83 PROTEIN DOWNREG. TU_0066742_0 chr1:154860755-154862200 0.42 −3.83 PROTEIN DOWNREG. TU_0090638_0 chr11:14242208-14246823 0.55 −3.83 PROTEIN DOWNREG. TU_0046626_0 chr4:3735533-3740037 0.46 −3.83 PROTEIN DOWNREG. TU_0024608_0 chr19:51842682-51856041 0.53 −3.83 PROTEIN DOWNREG. TU_0071146_0 chr20:25381375-25432639 0.58 −3.84 PROTEIN DOWNREG. TU_0080097_0 chr12:56301840-56307003 0.56 −3.85 PROTEIN DOWNREG. TU_0062615_0 chr1:48974664-48997227 0.51 −3.85 PROTEIN DOWNREG. TU_0013669_0 chr7:150272983-150305963 0.52 −3.86 PROTEIN DOWNREG. TU_0102682_0 chr9:70197177-70337519 0.56 −3.86 PROTEIN DOWNREG. TU_0104855_0 chr9:131689287-131691419 0.64 −3.86 PROTEIN DOWNREG. TU_0116336_0 chr2:48677181-48685259 0.65 −3.86 PROTEIN DOWNREG. TU_0116619_0 chr2:60532630-60533546 0.47 −3.87 PROTEIN DOWNREG. TU_0034452_0 chr14:69415893-69568826 0.48 −3.87 PROTEIN DOWNREG. TU_0067213_0 chr1:163086189-163087684 0.59 −3.87 PROTEIN DOWNREG. TU_0065337_0 chr1:148457403-148475119 0.56 −3.87 NOVEL DOWNREG. TU_0062461_0 chr1:46461750-46463004 0.51 −3.88 PROTEIN DOWNREG. TU_0080098_0 chr12:56302807-56307707 0.56 −3.88 PROTEIN DOWNREG. TU_0034421_0 chr14:68410559-68412495 0.62 −3.88 PROTEIN DOWNREG. TU_0016601_0 chr17:36911114-36928728 0.39 −3.88 PROTEIN DOWNREG. TU_0079221_0 chr12:51194638-51200498 0.43 −3.89 PROTEIN DOWNREG. TU_0112752_0 chr15:76184009-76210733 0.55 −3.90 PROTEIN DOWNREG. TU_0028410_0 chrX:48910899-48929704 0.68 −3.91 PROTEIN DOWNREG. TU_0076498_0 chr10:123227854-123347940 0.55 −3.92 NOVEL DOWNREG. TU_0093208_0 chr11:65396931-65397655 0.45 −3.92 PROTEIN DOWNREG. TU_0078129_0 chr12:27016771-27017190 0.47 −3.92 PROTEIN DOWNREG. TU_0064620_0 chr1:111962071-112059304 0.61 −3.92 PROTEIN DOWNREG. TU_0005224_0 chr6:107917248-108088034 0.60 −3.93 PROTEIN DOWNREG. TU_0023668_0 chr19:44114820-44158190 0.56 −3.93 PROTEIN DOWNREG. TU_0041856_0 chr3:190990156-191097717 0.44 −3.93 PROTEIN DOWNREG. TU_0107364_0 chr22:36658502-36671784 0.62 −3.93 PROTEIN DOWNREG. TU_0079224_0 chr12:51194638-51199100 0.43 −3.94 PROTEIN DOWNREG. TU_0027357_0 chrX:17728093-17737982 0.57 −3.94 PROTEIN DOWNREG. TU_0071013_0 chr20:19141491-19652034 0.55 −3.95 PROTEIN DOWNREG. TU_0060281_0 chr1:27204050-27211524 0.48 −3.95 PROTEIN DOWNREG. TU_0096007_0 chr11:119487208-119514087 0.45 −3.95 PROTEIN DOWNREG. TU_0058810_0 chr1:11631005-11637486 0.50 −3.95 ncRNA DOWNREG. TU_0102668_0 chr9:67902293-67904671 0.52 −3.96 PROTEIN DOWNREG. TU_0103126_0 chr9:93524079-93559558 0.55 −3.96 PROTEIN DOWNREG. TU_0098384_0 chr8:68508843-68581618 0.43 −3.96 NOVEL DOWNREG. TU_0084058_0 chr5:9602147-9603383 0.49 −3.96 ncRNA DOWNREG. TU_0018887_0 chr17:73068191-73068659 0.29 −3.97 PROTEIN DOWNREG. TU_0020916_0 chr19:9720305-9727203 0.55 −3.97 PROTEIN DOWNREG. TU_0018819_0 chr17:72184340-72195820 0.59 −3.97 NOVEL DOWNREG. TU_0042081_0 chr3:197374550-197376798 0.46 −3.97 PROTEIN DOWNREG. TU_0065864_0 chr1:149850009-149852238 0.46 −3.98 PROTEIN DOWNREG. TU_0111301_0 chr15:61676589-51684028 0.54 −3.98 PROTEIN DOWNREG. TU_0073443_0 chr10:5556713-3558609 0.43 −3.99 PROTEIN DOWNREG. TU_0030581_0 chrX:118096546-118104692 0.38 −3.99 PROTEIN DOWNREG. TU_0039780_0 chr3:120843508-120866813 0.55 −4.00 PROTEIN DOWNREG. TU_0081660_0 chr12:108705678-108718771 0.50 −4.00 PROTEIN DOWNREG. TU_0046397_0 chr4:2032569-2050090 0.46 −4.00 PROTEIN DOWNREG. TU_0122440_0 chr2:219991398-219999705 0.53 −4.01 PROTEIN DOWNREG. TU_0011534_0 chr7:99083477-99096154 0.36 −4.01 PROTEIN DOWNREG. TU_0047206_0 chr4:37815997-37817190 0.59 −4.02 PROTEIN DOWNREG. TU_0017005_0 chr17:39308253-39337366 0.52 −4.02 PROTEIN DOWNREG. TU_0052436_0 chr16:15704489-15858435 0.54 −4.03 PROTEIN DOWNREG. TU_0014761_0 chr17:7128572-7131411 0.46 −4.03 PROTEIN DOWNREG. TU_0080075_0 chr12:56290183-56301803 0.53 −4.03 PROTEIN DOWNREG. TU_0089295_0 chr5:177597111-177621358 0.48 −4.03 PROTEIN DOWNREG. TU_0062594_0 chr16:19775320-19780719 0.60 −4.03 PROTEIN DOWNREG. TU_0068168_0 chr1:199700556-199742901 0.61 −4.04 ncRNA DOWNREG. TU_0102657_0 chr9:67902293-67908869 0.54 −4.04 PROTEIN DOWNREG. TU_0003729_0 chr6:43525496-43528789 0.55 −4.04 PROTEIN DOWNREG. TU_0071246_0 chr20:29913077-29921837 0.42 −4.05 NOVEL DOWNREG. TU_0050224_0 chr4:147115887-147190781 0.25 −4.06 PROTEIN DOWNREG. TU_0110166_0 chr15:43172154-43198892 0.49 −4.07 PROTEIN DOWNREG. TU_0030085_0 chrX:101782933-101800062 0.56 −4.07 PROTEIN DOWNREG. TU_0021042_0 chr19:10435466-10441506 0.61 −4.08 PROTEIN DOWNREG. TU_0097463_0 chr8:37812227-37826549 0.58 −4.08 PROTEIN DOWNREG. TU_0101681_0 chr9:734412-736069 0.67 −4.08 PROTEIN DOWNREG. TU_0030157_0 chrX:102750729-102751737 0.44 −4.09 NOVEL DOWNREG. TU_0098190_0 chr8:61704765-61708199 0.40 −4.09 PROTEIN DOWNREG. TU_0062947_0 chr1:53744955-53838542 0.42 −4.09 PROTEIN DOWNREG. TU_0078008_0 chr12:21679541-21702042 0.57 −4.09 PROTEIN DOWNREG. TU_0017582_0 chr17:45858594-45907395 0.54 −4.09 PROTEIN DOWNREG. TU_0000021_0 chr6:1555144-1559122 0.53 −4.09 PROTEIN DOWNREG. TU_0031424_0 chrX:149432223-149433104 0.47 −4.10 PROTEIN DOWNREG. TU_0065603_0 chr1:149275738-149286201 0.42 −4.10 PROTEIN DOWNREG. TU_0037859_0 chr3:45240966-45242817 0.49 −4.11 PROTEIN DOWNREG. TU_0102271_0 chr9:34511045-34512853 0.50 −4.11 PROTEIN DOWNREG. TU_0035605_0 chr14:93254401-93273368 0.49 −4.11 PROTEIN DOWNREG. TU_0064621_0 chr1:112047963-112062396 0.54 −4.11 ncRNA DOWNREG. TU_0031098_0 chrX:134057388-134058604 0.47 −4.11 PROTEIN DOWNREG. TU_0018799_0 chr17:72061371-72080938 0.61 −4.11 PROTEIN DOWNREG. TU_0011129_0 chr7:94135058-94136943 0.41 −4.11 NOVEL DOWNREG. TU_0036396_0 chr14:104617328-104619095 0.41 −4.12 PROTEIN DOWNREG. TU_0086255_0 chr5:92944260-92956054 0.57 −4.12 ncRNA DOWNREG. TU_0074501_0 chr10:60429298-60431091 0.42 −4.12 PROTEIN DOWNREG. TU_0073757_0 chr10:17672547-17699461 0.56 −4.13 PROTEIN DOWNREG. TU_0015457_0 chr17:19581898-19587356 0.45 −4.13 PROTEIN DOWNREG. TU_0122402_0 chr2:219821926-219824741 0.61 −4.13 PROTEIN DOWNREG. TU_0116618_0 chr2:60532830-60633902 0.49 −4.13 PROTEIN DOWNREG. TU_0029963_0 chrX:100220537-100238005 0.51 −4.15 PROTEIN DOWNREG. TU_0028949_0 chrX:64804077-64878518 0.61 −4.15 PROTEIN DOWNREG. TU_0088443_0 chr5:154178336-154210363 0.57 −4.16 PROTEIN DOWNREG. TU_0107371_0 chr22:36668731-36671784 0.56 −4.17 PROTEIN DOWNREG. TU_0016830_0 chr17:38070906-38071660 0.57 −4.17 PROTEIN DOWNREG. TU_0016596_0 chr17:36923524-36946925 0.50 −4.17 PROTEIN DOWNREG. TU_0014764_0 chr17:7131441-7134452 0.45 −4.18 PROTEIN DOWNREG. TU_0070473_0 chr20:2621571-2702522 0.60 −4.18 PROTEIN DOWNREG. TU_0065602_0 chr1:149282206-149286718 0.40 −4.19 PROTEIN DOWNREG. TU_0105435_0 chr9:138997874-138999099 0.37 −4.19 PROTEIN DOWNREG. TU_0015445_0 chr17:19415396-19422913 0.46 −4.20 PROTEIN DOWNREG. TU_0019012_0 chr17:74597027-74990278 0.42 −4.21 PROTEIN DOWNREG. TU_0048538_0 chr4:81336928-81344460 0.41 −4.22 PROTEIN DOWNREG. TU_0098385_0 chr8:68508843-68509111 0.41 −4.22 PROTEIN DOWNREG. TU_0076499_0 chr10:123227854-123248042 0.53 −4.23 PROTEIN DOWNREG. TU_0117482_0 chr2:73973507-74000287 0.56 −4.23 PROTEIN DOWNREG. TU_0114778_0 chr2:20264034-20288661 0.45 −4.24 PROTEIN DOWNREG. TU_0018316_0 chr17:33917848-33935788 0.53 −4.25 PROTEIN DOWNREG. TU_0071893_0 chr20:34603301-34611746 0.59 −4.25 PROTEIN DOWNREG. TU_0073523_0 chr10:8136827-8157157 0.44 −4.26 PROTEIN DOWNREG. TU_0064500_0 chr1:110061334-110079791 0.42 −4.27 PROTEIN DOWNREG. TU_0065862_0 chr1:149850009-149852444 0.41 −4.27 PROTEIN DOWNREG. TU_0030064_0 chrX:101268429-101269091 0.44 −4.28 PROTEIN DOWNREG. TU_0060278_0 chr1:27192773-27200190 0.51 −4.28 PROTEIN DOWNREG. TU_0000013_0 chr6:1257191-1259972 0.36 −4.29 PROTEIN DOWNREG. TU_0120707_0 chr2:176665581-176669190 0.46 −4.31 PROTEIN DOWNREG. TU_0016744_0 chr17:37790368-37809206 0.54 −4.31 PROTEIN DOWNREG. TU_0016827_0 chr17:38065830-38071660 0.63 −4.31 PROTEIN DOWNREG. TU_0056190_0 chr18:26824024-26842486 0.43 −4.33 PROTEIN DOWNREG. TU_0096964_0 chr8:22027917-22043914 0.47 −4.35 PROTEIN DOWNREG. TU_0030062_0 chrX:101267701-101269091 0.41 −4.36 ncRNA DOWNREG. TU_0120711_0 chr2:176690351-176696560 0.49 −4.36 PROTEIN DOWNREG. TU_0011537_0 chr7:99085728-99111736 0.39 −4.39 PROTEIN DOWNREG. TU_0107366_0 chr22:36668731-36673469 0.54 −4.39 PROTEIN DOWNREG. TU_0065341_0 chr1:148496551-148500610 0.35 −4.39 PROTEIN DOWNREG. TU_0015076_0 chr17:12510065-12612990 0.50 −4.40 PROTEIN DOWNREG. TU_0087752_0 chr5:139206352-139211418 0.44 −4.40 PROTEIN DOWNREG. TU_0108990_0 chr15:34970176-35180015 0.51 −4.41 PROTEIN DOWNREG. TU_0062566_0 chr1:47037330-47057598 0.43 −4.42 PROTEIN DOWNREG. TU_0018825_0 chr17:72192513-72192794 0.47 −4.43 PROTEIN DOWNREG. TU_0002566_0 chr6:33797424-33798978 0.37 −4.44 PROTEIN DOWNREG. TU_0074074_0 chr10:29814868-29815135 0.26 −4.44 PROTEIN DOWNREG. TU_0110179_0 chr15:43196205-43235205 0.43 −4.46 PROTEIN DOWNREG. TU_0082372_0 chr12:116130336-116130610 0.41 −4.47 ncRNA DOWNREG. TU_0102658_0 chr9:67902293-67908683 0.46 −4.48 PROTEIN DOWNREG. TU_0024160_0 chr19:48777171-48778386 0.51 −4.49 PROTEIN DOWNREG. TU_0031081_0 chrX:133993992-134013925 0.64 −4.49 PROTEIN DOWNREG. TU_0015447_0 chr17:19421649-19423000 0.46 −4.50 PROTEIN DOWNREG. TU_0016834_0 chr17:38072130-38072515 0.54 −4.50 PROTEIN DOWNREG. TU_0120709_0 chr2:176677352-176697902 0.49 −4.50 PROTEIN DOWNREG. TU_0041205_0 chr3:171619688-171634575 0.48 −4.53 PROTEIN DOWNREG. TU_0110178_0 chr15:43196270-43241274 0.43 −4.54 PROTEIN DOWNREG. TU_0064473_0 chr1:110000292-110079791 0.51 −4.58 ncRNA DOWNREG. TU_0120715_0 chr2:176692475-176697902 0.50 −4.58 PROTEIN DOWNREG. TU_0110180_0 chr15:43196205-43243358 0.43 −4.63 PROTEIN DOWNREG. TU_0024922_0 chr19:54253368-54259943 0.42 −4.64 ncRNA DOWNREG. TU_0115816_0 chr2:38109039-38116939 0.32 −4.64 ncRNA DOWNREG. TU_0067289_0 chr1:166307141-166318970 0.48 −4.69 NOVEL DOWNREG. TU_0095765_0 chr11:117640504-117642734 0.36 −4.69 PROTEIN DOWNREG. TU_0058445_0 chr1:9017797-9040122 0.33 −4.70 PROTEIN DOWNREG. TU_0047068_0 chr4:23402764-23403824 0.41 −4.72 PROTEIN DOWNREG. TU_0016882_0 chr17:38260060-38263683 0.51 −4.82 NOVEL DOWNREG. TU_0098382_0 chr8:68494189-68495887 0.29 −4.83 PROTEIN DOWNREG. TU_0110177_0 chr15:43196768-43245735 0.47 −4.86 PROTEIN DOWNREG. TU_0089598_0 chr11:303980-310982 0.35 −4.87 PROTEIN DOWNREG. TU_0107527_0 chr22:37740155-37746215 0.44 −4.88 PROTEIN DOWNREG. TU_0107528_0 chr22:37741248-37746215 0.43 −4.90 PROTEIN DOWNREG. TU_0032311_0 chr14:23612588-23617134 0.32 −5.04

TABLE 5 Fold change Expected score Observed (PCA vs q-value PCAT ID GeneChromosomal Location (dExp) score (d) Benign (%) PCAT-1 TU_0099865_0chr8: 128087842-128095202 −2.2654014 5.444088 6.9071784 0 PCAT-2TU_0090142_0 chr11: 4748677-4760303 −2.4408573 4.6781354 11.39658 0PCAT-3 TU_0054603_0 chr16: 82380933-82394836 −2.1786723 4.46124555.8916535 0 PCAT-4 TU_0090140_0 chr11: 4748163-4759145 −2.1153426 4.43457.1933164 0 PCAT-5 TU_0078288_0 chr12: 32393283-32405731 −1.91642194.312603 3.5655262 0 PCAT-6 TU_0099864_0 chr6: 128094589-128103681−1.7214081 4.265536 3.8937242 0 PCAT-7 TU_0084308_0 chr5:15938753-15949124 −1.9636476 4.124071 4.747601 0 PCAT-8 TU_0084303_0chr5: 15899476-15955226 −2.0245786 4.0520086 7.1035967 0 PCAT-9TU_0082746_0 chr12: 120197102-120197416 −1.861408 3.7551165 5.1431665 0PCAT-10 TU_0078296_0 chr12: 32394534-32405549 −1.5944241 3.69029143.034359 0 PCAT-11 TU_0078290_0 chr12: 32394534-32410898 −1.53379543.675318 3.1572607 0 PCAT-12 TU_0002597_0 chr6: 34335202-34338521−1.6263148 3.6469774 3.352418 0 PCAT-13 TU_0049368_0 chr4:106772318-106772770 −1.6894234 3.6079373 2.8299546 0 PCAT-14TU_0106548_0 chr22: 22209111-22212055 −1.939075 3.591358 5.962547 0PCAT-15 TU_0078293_0 chr12: 32396393-32414822 −1.5212961 3.57059452.9213174 0 PCAT-16 TU_0099884_0 chr8: 128301493-128307576 −1.44450643.5658643 2.516981 0 PCAT-17 TU_0112014_0 chr15: 67722165-67739990−1.6326295 3.562463 3.694224 0 PCAT-18 TU_0084306_0 chr5:15896315-15947088 −1.845 3.5603588 5.746707 0 PCAT-19 TU_0114240_0 chr2:1534883-1538193 −1.6870209 3.5233572 4.339847 0 PCAT-20 TU_0008499_0chr7: 24236191-24236455 −1.8302058 3.5071697 6.6821446 0 PCAT-21TU_0078299_0 chr12: 32290896-32292169 −1.7297353 3.506232 3.2923684 0PCAT-22 TU_0000033_0 chr6: 1619606-1668581 −1.7680657 3.434188 2.24708180 PCAT-23 TU_0096472_0 chr11: 133844590-133862924 −1.8782617 3.4103555.9854193 0 PCAT-24 TU_0114259_0 chr2: 1606782-1607314 −1.66623773.3919659 5.060926 0 PCAT-25 TU_0096473_0 chr11: 133844590-133862995−1.8963361 3.3859823 6.1071715 0 PCAT-26 TU_0100361_0 chr8:144914456-144930753 −1.6521469 3.3805158 3.8420231 0 PCAT-27TU_0040394_0 chr3: 133418632-133441282 −1.6208398 3.3201025 2.9724674 0PCAT-28 TU_0043432_0 chr13: 34032994-34050503 −1.6739471 3.20375513.2093527 0 PCAT-29 TU_0112020_0 chr15: 67764259-67801825 −1.56033163.1967351 3.593551 0 PCAT-30 TU_0042717_0 chr13: 23149908-23200198−2.0654948 3.1685438 4.9699407 0 PCAT-31 TU_0078292_0 chr12:32290485-32406307 −1.4503003 3.151879 2.8911364 0 PCAT-32 TU_0084146_0chr5: 14025126-14062770 −1.6452767 3.1257985 2.6190455 0 PCAT-33TU_0056168_0 chr18: 22477042-22477666 −1.5381516 3.0557241 3.1951044 0PCAT-34 TU_0040383_0 chr3: 133360541-133429262 −1.5558791 3.04165083.7478442 0 PCAT-35 TU_0112025_0 chr15: 67780574-87782345 −1.68153773.0412362 3.433415 0 PCAT-36 TU_0041688_0 chr3: 186741299-186741933−1.4749297 3.0062308 2.543468 0 PCAT-37 TU_0103642_0 chr9:109187089-109187455 −1.7387192 2.998956 6.6124363 0 PCAT-38 TU_0040375_0chr3: 133280694-133394609 −1.5469999 2.9753568 3.9068055 0 PCAT-39TU_0047312_0 chr4: 39217669-39222163 −1.6388936 2.9124916 3.6121209 0PCAT-40 TU_0106545_0 chr22: 22218478-22219162 −1.7586497 2.8898563.7357745 0 PCAT-41 TU_0054541_0 chr16: 79408800-79435066 −1.74859342.8699164 6.647557 0 PCAT-42 TU_0060446_0 chr1: 28438629-28450156−1.4880521 2.857332 1.9824111 0 PCAT-43 TU_0072907_0 chr20:55759486-55771563 −1.5254781 2.7966201 2.812179 0 PCAT-44 TU_0043403_0chr13: 33844637-33845921 −1.5793877 2.7919009 3.6403422 0 PCAT-45TU_0038678_0 chr3: 53515951-53517078 −1.7047809 2.7858517 3.6908987 0PCAT-46 TU_0101706_0 chr9: 3408690-3415374 −1.4780945 2.78220993.3066912 0 PCAT-47 TU_0101709_0 chr9: 3411967-3415374 −1.46523732.7622206 3.1886175 0 PCAT-48 TU_0106544_0 chr22: 22210421-22220506−1.6153399 2.7578135 3.7418716 0 PCAT-49 TU_0046121_0 chr4:766363-766599 −1.5697786 2.7573307 1.485532 0 PCAT-50 TU_0106542_0chr22: 22211315-22220506 −1.6098742 2.755721 3.3781004 0 PCAT-51TU_0106541_0 chr22: 22209111-22219162 −1.6593723 2.7341027 3.664146 0PCAT-52 TU_0044453_0 chr13: 51505777-51524522 −1.3416 2.732019 2.5369530 PCAT-53 TU_0104717_0 chr9: 130697833-130698832 −1.2938 2.72197322.3344588 0 PCAT-54 TU_0089014_0 chr5: 176014905-176015351 −1.39678732.7047238 1.7803582 0 PCAT-55 TU_0108452_0 chr15: 19344745-19362916−1.5839852 2.6759455 1.8484153 0 PCAT-56 TU_0112003_0 chr15:67645590-67775246 −1.4386703 2.668052 3.045022 0 PCAT-57 TU_0078286_0chr12: 32395588-32405731 −1.3580605 2.6660874 2.6121044 0 PCAT-58TU_0078303_0 chr12: 32274210-32274530 −1.5020599 2.65866 3.3306372 0PCAT-59 TU_0112004_0 chr15: 67644390-67650387 −1.5175762 2.65098882.9933636 0 PCAT-60 TU_0071087_0 chr20: 21428679-21429454 −1.49166882.649109 4.6481714 0 PCAT-61 TU_0072906_0 chr20: 55759768-55770657−1.5059631 2.645004 2.95756 0 PCAT-62 TU_0054240_0 chr16:70155175-70173873 −1.4715649 2.6437716 3.5309577 0 PCAT-63 TU_0047330_0chr4: 39217641-39222163 −1.5139307 2.6277235 3.0695639 0 PCAT-64TU_0055435_0 chr18: 6715938-6719172 −1.6048826 2.6173768 2.9221427 0PCAT-65 TU_0079791_0 chr12: 54971063-54971481 −1.4415668 2.60108232.0141602 0 PCAT-66 TU_0043411_0 chr13: 33918267-33926769 −1.4950642.5991623 3.3860362 0 PCAT-67 TU_0056121_0 chr18: 20196762-20197522−1.2526748 2.5938754 1.7191441 0 PCAT-68 TU_0043412_0 chr13:33918267-33935946 −1.5891836 2.590199 4.2804046 0 PCAT-69 TU_0065837_0chr1: 149791252-149795934 −1.3852053 2.5882297 2.9343975 0 PCAT-70TU_0043401_0 chr13: 33825711-33845275 −1.5994886 2.5853698 4.3461533 0PCAT-71 TU_0006463_0 chr6: 144659819-144660143 −1.4985942 2.57441072.2007995 0 PCAT-72 TU_0048506_0 chr4: 80329017-80348259 −1.57443822.5690413 2.8022916 0 PCAT-73 TU_0084140_0 chr5: 14003669-14054874−1.4040573 2.5472755 2.5979335 0 PCAT-74 TU_0082982_0 chr12:121776584-121777370 −1.5293782 2.5458217 2.6197503 0 PCAT-75TU_0013212_0 chr7: 138990883-139001515 −1.2296493 2.544434 1.6879753 0PCAT-76 TU_0072912_0 chr20: 55779532-55780817 −1.4302964 2.54067373.8653345 0 PCAT-77 TU_0112281_0 chr15: 70586704-70590792 −1.45901552.5375097 2.4288568 0 PCAT-78 TU_0048767_0 chr4: 88120066-88124880−1.3735119 2.5323946 2.233308 0 PCAT-79 TU_0108455_0 chr15:19358326-19365341 −1.5651321 2.5261333 1.9462687 0 PCAT-80 TU_0091997_0chr11: 58560356-58573012 −1.3149309 2.5185204 2.1176686 0 PCAT-81TU_0121655_0 chr2: 202985284-202998634 −1.4014161 2.476237 2.21941880.859614 PCAT-82 TU_0071798_0 chr20: 33775260-33778511 −1.33566652.4645917 1.6566333 0.850371 PCAT-83 TU_0049200_0 chr4:102469973-102476087 −1.3222212 2.456723 1.9456172 0.841324 PCAT-84TU_0121714_0 chr2: 203295212-203314868 −1.3457565 2.4496663 1.76242740.832468 PCAT-85 TU_0098937_0 chr8: 95748751-95751321 −1.4532137 2.422482.2326834 0.823797 PCAT-86 TU_0108453_0 chr15: 19356996-19364013−1.8033699 2.4094539 3.839975 0.767811 PCAT-87 TU_0114170_0 chr15:99659312-99669199 −1.4358851 2.4062114 2.1252658 0.768711 PCAT-88TU_0089906_0 chr11: 1042845-1045705 −1.3899238 2.401665 2.63909550.767811 PCAT-89 TU_0001559_0 chr6: 30283700-30286011 −1.35170652.3987799 1.5110766 0.767811 PCAT-90 TU_0050557_0 chr4:159976338-160016453 −1.17525 2.398688 2.0524442 0.767811 PCAT-91TU_0078294_0 chr12: 32395632-32413064 −1.4560982 2.3969867 2.18632080.767811 PCAT-92 TU_0044933_0 chr13: 94755992-94760688 −1.29051972.3965187 2.189938 0.767811 PCAT-93 TU_0017730_0 chr17:52346638-52346880 −1.4169512 2.3874657 1.4708191 0.760428 PCAT-94TU_0039020_0 chr3: 66578329-66607777 −1.2662895 2.3720088 1.71127090.712473 PCAT-95 TU_0049213_0 chr4: 102461960-102476087 −1.27251392.3671806 1.8876821 0.712473 PCAT-96 TU_0093070_0 chr11:64945809-64961189 −1.2954472 2.3645105 1.9128969 0.712473 PCAT-97TU_0051063_0 chr4: 187244297-187244767 1.8922831 −2.8485844 0.509831550.732264 PCAT-98 TU_0098190_0 chr8: 61704765-61708199 1.9825526−2.8612607 0.4027831 0.732264 PCAT-99 TU_0038811_0 chr3:57890130-57890834 1.9620296 −2.8837616 0.44431657 0.732264 PCAT-100TU_0020914_0 chr19: 9718612-9721799 1.6433232 −2.9243097 0.506230060.732264 PCAT-101 TU_0112056_0 chr15: 69658838-69678469 1.837821−3.0355222 0.46161976 0 PCAT-102 TU_0036396_0 chr14: 104617328-1046190951.849786 −3.1192882 0.45514825 0 PCAT-103 TU_0095765_0 chr11:117640504-117642734 2.1002219 −3.2632742 0.38160667 0 PCAT-104TU_0050224_0 chr4: 147115887-147190781 2.1981242 −3.2975357 0.28569755 0PCAT-105 TU_0112059_0 chr15: 69667695-69691724 1.8148681 −3.38166260.43667468 0 PCAT-106 TU_0098382_0 chr8: 68494189-68495887 2.5413978−4.0586042 0.30793378 0

TABLE 6 Median Maximum Expression Expression PCAT ID Gene ChromosomalLocation Outlier Score (RPKM) (RPKM) PCAT-107 TU_0029004_0 chrX:66691350-66692032 130.7349145 1 90.921 PCAT-108 TU_0054542_0 chr16:79420131-79423590 127.0430957 5.60998 135.85 PCAT-109 TU_0120899_0 chr2:180689090-180696402 123.5416436 1.0525222 94.6932 PCAT-110 TU_0054540_0chr16: 79419351-79423673 119.090847 4.161985 94.4461 PCAT-111TU_0120918_0 chr2: 181297540-181400892 112.710111 1.4533705 92.1795PCAT-112 TU_0054538_0 chr16: 79408946-79450819 98.01851659 1.83034393.1207 PCAT-113 TU_0059541_0 chr1: 20685471-20686432 68.35725071.783109 1375.15 PCAT-114 TU_0120924_0 chr2: 181331111-18142748563.95455962 1.3891845 365.202 PCAT-115 TU_0074308_0 chr10:42652247-42653596 60.91841567 1.393607 65.7712 PCAT-116 TU_0049192_0chr4: 102257900-102306678 59.24997694 1.3854525 69.2423 PCAT-117TU_0054537_0 chr16: 79406933-79430041 58.04481977 1.8534395 42.751PCAT-118 TU_0120900_0 chr2: 180926864-180985967 55.8438747 1 67.6582PCAT-119 TU_0114527_0 chr2: 10858318-10858530 54.76455104 1.296977535.0059 PCAT-120 TU_0120923_0 chr2: 181328093-181419226 52.97932271.2821 232.556 PCAT-121 TU_0049231_0 chr4: 102257900-10225969552.77001947 1.34042 67.6276

TABLE 7 Median Maximum Outlier Expression Expression Rank GeneChromosomal location Score (RPKM) (RPKM) 1 CRISP3 chr6:49803053-49813070 294.56446 1.5414775 478.812 2 SPINK1 chr5:147184335-147191453 177.19518 2.484455 624.733 3 TU_0029004_0 chrX:66691350-66692032 130.73491 1 90.921 4 TU_0054542_0 chr16:79420131-79423590 127.0431 5.60998 135.85 5 TU_0120899_0 chr2:180689090-180696402 123.54164 1.0525222 94.6932 6 ERG chr21:38673821-38792298 119.446 3.421615 178.826 7 TU_0054540_0 chr16:79419351-79423673 119.09085 4.161985 94.4461 8 ERG chr21:38673821-38792298 117.60294 3.470755 176.186 9 ERG chr21:38673821-38955574 117.26408 3.385695 170.663 10 ERG chr21:38673821-38955574 116.33448 3.40077 170.443 11 TU_0120918_0 chr2:181297540-181400892 112.71011 1.4533705 92.1795 12 C7orf68 chr7:127883119-127885708 105.18504 6.835525 336.148 13 CSRP3 chr11:19160153-19180106 101.12947 1 148.45 14 C7orf68 chr7:127883119-127885708 100.63202 7.08303 337.76 15 COL2A1 chr12:46653014-46684552 99.166329 1.2285615 96.0977 16 C1orf64 chr1:16203317-16205771 98.085922 3.62012 252.013 17 TU_0054538_0 chr16:79408946-79450819 98.018517 1.830343 93.1207 18 COL2A1 chr12:46653014-46684552 97.347905 1.2416035 94.6672 19 CSRP3 chr11:19160153-19180165 96.730187 1 141.963 20 COL9A2 chr1: 40538749-4055552674.408443 19.24815 570.961 21 PLA2G7 chr6: 46780012-46811389 69.52117510.83567 97.8331 22 AGT chr1: 228904891-228916959 69.319886 4.797365189.281 23 TU_0059541_0 chr1: 20685471-20686432 68.357251 1.7831091375.15 24 ETV1 chr7: 13897382-13992664 68.218569 1.932797 138.519 25ETV1 chr7: 13897382-13992664 67.723331 1.9899945 142.406 26 ETV1 chr7:13897382-13992664 67.680571 1.9915925 143.632 27 PLA2G7 chr6:46780011-46811110 67.089039 10.62 95.3551 28 ETV1 chr7:13897382-13997390 66.381191 2.097225 143.975 29 ETV1 chr7:13897382-13997575 65.563724 2.074935 141.069 30 MUC6 chr11:1002823-1026706 64.7328 1.466194 351.862 31 TU_0120924_0 chr2:181331111-181427485 63.95456 1.3891845 365.202 32 ETV1 chr7:13897382-13996167 63.929225 2.05648 135.131 33 ETV1 chr7:13897382-13996167 62.424072 2.03086 131.644 34 TU_0074308_0 chr10:42652247-42653596 60.918416 1.393607 65.7712 35 TU_0049192_0 chr4:102257900-102306678 59.249977 1.3854525 69.2423 36 TU_0054537_0 chr16:79406933-79430041 58.04482 1.8534395 42.751 37 RGL3 chr19:11365731-11391018 57.528689 7.660035 91.2238 38 RGL3 chr19:11365731-11391018 57.393056 7.6327 90.6937 39 TMEM45B chr11:129190950-129235108 55.887845 4.87695 60.0414 40 TU_0120900_0 chr2:180926864-180985967 55.843875 1 67.6582 41 PTK6 chr20: 61630219-6163915155.101291 3.420545 114.116 42 TU_0114527_0 chr2: 10858318-1085853054.764551 1.2969775 35.0059 43 TU_0112020_0 chr15: 67764259-6780182553.882769 2.0281615 88.99 44 TU_0120923_0 chr2: 181328093-18141922652.979323 1.2821 232.556 45 TU_0049231_0 chr4: 102257900-10225969552.770019 1.34042 67.6276 46 MON1B chr16: 75782336-75791044 51.71702726.00355 187.807 47 TU_0054541_0 chr16: 79408800-79435066 50.4452481.7164375 32.5832 48 TU_0087466_0 chr5: 136779809-136798173 50.2851691.2738505 42.0309 49 DLX1 chr2: 172658453-172662647 50.048039 2.08862543.0035 50 TU_0108209_0 chr22: 46493579-46531245 47.753833 1.049141926.6643 51 DLX1 chr2: 172658453-172662647 47.159314 1.9682735 38.4705 52SMC4 chr3: 161600123-161635435 47.127047 4.581655 63.2353 53 SMC4 chr3:161601040-161635435 46.967013 4.442065 61.2756 54 TU_0102399_0 chr9:35759438-35761676 46.664973 6.44675 179.711 55 TU_0029005_0 chrX:66690414-66704178 46.155567 1.0870047 38.3022 56 C15orf48 chr15:43510054-43512939 45.732195 19.02125 223.42 57 C15orf48 chr15:43510054-43512939 45.549287 21.28355 248.097 58 EFNA3 chr1:153317971-153326638 44.993943 3.68358 70.5016 59 TU_0043412_0 chr13:33918267-33935946 44.506741 1.311142 15.1968 60 TU_0069093_0 chr1:220878648-220886461 42.645673 1.443496 160.898 61 UGT1A6 chr2:234265059-234346684 42.500058 1.937622 45.753 62 TU_0057051_0 chr18:54524352-54598419 42.108622 2.418785 56.0712 63 AMH chr19:2200112-2203072 41.744334 2.16026 91.244 64 TU_0120908_0 chr2:181147971-181168431 41.650097 1.0750564 48.7957 65 TU_0099873_0 chr8:128138926-128140075 41.420293 1.51101 38.7353 66 HN1 chr17:70642938-70662369 40.495209 16.35625 110.208 67 TU_0022570_0 chr19:20341299-20343938 39.984803 2.912835 98.5739 68 TU_0098937_0 chr8:95748751-95751321 39.740546 1.4422495 51.5935 69 TU_0040375_0 chr3:133280694-133394609 39.664781 2.149005 90.9787 70 HN1 chr17:70642938-70662370 39.655603 16.34725 109.587 71 TU_0120929_0 chr2:181328093-181423017 39.419483 1.2116475 189.765 72 TU_0112004_0 chr15:67644390-67650387 39.300923 6.10665 76.723 73 TU_0108439_0 chr15:19293567-19296333 39.131646 1 27.7534 74 HN1 chr17: 70642938-7066236939.00893 15.53595 103.782 75 SULT1C2 chr2: 108271526-108292803 39.0070621.2259165 91.5617 76 STX19 chr3: 95215904-95230144 38.954223 4.52125546.0375 77 TU_0030420_0 chrX: 112642982-112685485 38.715477 1.089078562.9419 78 TU_0099875_0 chr8: 128138047-128140075 38.489447 1.39341335.8984 79 UBE2T chr1: 200567408-200577717 38.387515 3.070345 85.9738 80SULT1C2 chr2: 108271526-108292803 37.817555 1.215033 88.0858 81TU_0049429_0 chr4: 109263508-109272353 37.794245 1.09915225 29.1838 82STMN1 chr1: 26099193-26105955 37.319869 14.3784 187.062 83 UGT1A1 chr2:234333657-234346684 37.267194 1.660554 35.9476 84 LRRN1 chr3:3816120-3864387 37.229013 3.8912 137.117 85 TU_0086631_0 chr5:113806149-113806936 36.896806 1.0501165 29.6561 86 ORM2 chr9:116131889-116135357 36.878688 3.614505 120.139 87 TU_0084060_0 chr5:7932238-7932523 36.807599 1 23.1979 88 TU_0098644_0 chr8:81204784-81207034 36.779294 1.6013735 64.9663 89 ACSM1 chr16:20542059-20610079 36.280896 13.3707 317.077 90 STMN1 chr1:26099193-26105231 35.882914 12.73275 164.721 91 STMN1 chr1:26099193-26105580 35.823453 14.31935 185.329 92 TU_0120914_0 chr2:181265370-181266053 35.551458 1.053468 30.7074 93 UGT1A7 chr2:234255322-234346684 35.073998 1.667349 33.4378 94 TU_0087462_0 chr5:136386339-136403134 34.992335 1.4450115 27.1703 95 UGT1A3 chr2:234302511-234346684 34.952247 1.6889365 33.4202 96 UGT1A5 chr2:234286376-234346684 34.950003 1.6639345 33.2718 97 FOXD1 chr5:72777840-72780108 34.875512 1.2373575 10.80944 98 ADM chr11:10283217-10285499 34.855767 11.83635 276.194 99 PPFIA4 chr1:201286933-201314487 34.769924 1.566044 43.9812 100 UGT1A10 chr2:234209861-234346690 34.738527 1.652799 32.7318 101 UGT1A4 chr2:234292176-234346684 34.663597 1.655824 32.9264 102 UGT1A9 chr2:234245282-234346690 34.648086 1.655272 32.852 103 TU_0090142_0 chr11:4748677-4760303 34.517072 1.6226305 51.3411 104 TU_0082746_0 chr12:120197102-120197416 34.499713 2.531095 59.9026 105 UGT1A8 chr2:234191029-234346684 34.433379 1.6498025 32.5849 106 TU_0112207_0 chr15:70278422-70286121 34.308752 10.40266 112.274 107 LOC145837 chr15:67641112-67650833 34.291574 7.59729 74.8194 108 TU_0050712_0 chr4:170217424-170228463 34.23107 1.504313 65.5606 109 TU_0043410_0 chr13:33929484-33944669 34.112491 1.393529 24.8401 110 SNHG1 chr11:62376035-62379936 33.971989 33.74365 270.512 111 MUC1 chr1:153424923-153429324 33.838228 16.3238 664.278 112 MUC1 chr1:153424923-153429324 33.823147 15.8436 644.44 113 TU_0099871_0 chr8:128138047-128143500 33.697285 1.412872 33.2958 114 TU_0040383_0 chr3:133360541-133429262 33.548813 2.553955 85.8384 115 MUC1 chr1:153424923-153429324 33.495501 15.91355 627.622 116 TU_0049202_0 chr4:102257900-102304755 33.391066 1.5555505 39.7522 117 TU_0120913_0 chr2:181254530-181266950 33.188328 1 43.8515 118 B4GALNT4 chr11:359794-372116 33.176248 6.3749 80.9639 119 TU_0100059_0 chr8:141258835-141260573 33.169029 1.3615865 44.8943 120 TOP2A chr17:35798321-35827695 33.132056 1.9725825 34.1032 121 MUC1 chr1:153424923-153429324 33.081326 15.9539 632.042 122 TU_0001265_0 chr6:27081719-27082291 33.045746 1.3381905 100.5401 123 C7orf53 chr7:111908143-111918171 33.024251 2.820945 32.2465 124 SLC45A2 chr5:33980477-34020537 32.952911 2.012104 54.8589 125 TU_0099869_0 chr8:128138047-128225937 32.928048 1.308804 30.4667 126 UGT1A6 chr2:234266250-234346690 32.918772 1.662221 31.4671 127 TU_0120917_0 chr2:181265370-181266950 32.796137 1.0771403 36.3557 128 CACNA1D chr3:53504070-53821532 32.608994 4.51306 44.9904 129 UBE2C chr20:43874661-43879003 32.456813 1.6391285 58.398 130 ALDOC chr17:23924259-23928078 32.455953 14.98415 228.812 131 MUC1 chr1:153424923-153429324 32.44845 15.5895 599.062 132 MMP11 chr22:22445035-22456503 32.411555 3.257735 73.9158 133 TU_0084303_0 chr5:15899476-15955226 32.39036 2.21168 14.4385 134 CACNA1D chr3:53504070-53821532 32.381439 4.484655 44.6867 135 UBE2C chr20:43874661-43879003 32.358151 1.705223 57.8559 136 CACNA1D chr3:53504070-53821532 32.353332 4.463805 44.2455 137 FGFRL1 chr4:995609-1010686 32.275762 26.0133 450.449 138 FGFRL1 chr4: 996251-101068632.075261 27.0148 468.809 139 FGFRL1 chr4: 995759-1010686 32.06990126.92945 467.246 140 MUC1 chr1: 153424923-153429324 32.011017 15.3218586.058 141 TU_0099922_0 chr8: 128979617-128981414 31.833339 3.3254432.6893 142 TU_0001173_0 chr6: 26385234-26386052 31.823293 2.33959571.3388 143 MUC1 chr1: 153424923-153429324 31.781267 15.22945 587.582144 TMEM178 chr2: 39746141-39798605 31.614406 13.40605 182.08 145 UBE2Cchr20: 43874661-43879003 31.37539 1.7154185 58.1531 146 KCNC2 chr12:73720162-73889778 31.294059 1.8783795 104.225 147 MAGEC2 chrX:141117794-141120742 31.286618 1 34.1099 148 SERHL2 chr22:41279868-41300332 31.131788 3.670135 61.9969 149 KCNC2 chr12:73720162-73889778 31.126593 1.868714 108.199 150 GRAMD4 chr22:45401321-45454352 31.063732 5.977725 79.8338

Table 8 shows the number of cancer-associated lncRNAs nominated for fourmajor cancer types. The number validated is indicated in the column onthe right. This table reflects ongoing efforts.

TABLE 8 # of cancer-specific # validated lncRNAs nominated to dateProstate cancer 121 11 Breast cancer 6 6 Lung cancer 36 32 Pancreaticcancer 34 0

All publications, patents, patent applications and accession numbersmentioned in the above specification are herein incorporated byreference in their entirety. Although the invention has been describedin connection with specific embodiments, it should be understood thatthe invention as claimed should not be unduly limited to such specificembodiments. Indeed, various modifications and variations of thedescribed compositions and methods of the invention will be apparent tothose of ordinary skill in the art and are intended to be within thescope of the following claims.

1-19. (canceled)
 20. A method of detecting non-coding RNAs (ncRNA) in asubject comprising (a) obtaining a sample from a subject suspected ofhaving prostate cancer, wherein the sample comprises ncRNA; (b)processing the sample to isolate or enrich the sample for ncRNA or cellscontaining ncRNA; and (c) detecting the level of expression of one ormore ncRNAs in said sample by sequencing, nucleic acid hybridization ornucleic acid amplification, wherein said one or more ncRNAs is selectedfrom the group consisting of one or more PCATs and SChLAP-1.
 21. Themethod of claim 20, wherein the one or more PCATs is selected from thegroup consisting of PCAT1, PCAT2, PCAT3, PCAT4, PCAT5, PCAT6, PCAT7,PCAT8, PCAT9, PCAT10, PCAT11, PCAT12, PCAT13, PCAT14, PCAT15, PCAT16,PCAT17, PCAT18, PCAT19, PCAT20, PCAT21, PCAT22, PCAT23, PCAT24, PCAT25,PCAT26, PCAT27, PCAT28, PCAT29, PCAT30, PCAT31, PCAT32, PCAT33, PCAT34,PCAT35, PCAT36, PCAT37, PCAT38, PCAT39, PCAT40, PCAT41, PCAT42, PCAT43,PCAT44, PCAT45, PCAT46, PCAT47, PCAT48, PCAT49, PCAT50, PCAT51, PCAT52,PCAT53, PCAT54, PCAT55, PCAT56, PCAT57, PCAT58, PCAT59, PCAT60, PCAT61,PCAT62, PCAT63, PCAT64, PCAT65, PCAT66, PCAT67, PCAT68, PCAT69, PCAT70,PCAT71, PCAT72, PCAT73, PCAT74, PCAT75, PCAT76, PCAT77, PCAT78, PCAT79,PCAT80, PCAT81, PCAT82, PCAT83, PCAT84, PCAT85, PCAT86, PCAT87, PCAT88,PCAT89, PCAT90, PCAT91, PCAT92, PCAT93, PCAT94, PCAT95, PCAT96, PCAT97,PCAT98, PCAT99, PCAT100, PCAT101, PCAT102, PCAT103, PCAT104, PCAT105,PCAT106, PCAT107, PCAT108, PCAT109, PCAT110, PCAT111, PCAT112, PCAT113,PCAT114, PCAT115, PCAT116, PCAT117, PCAT118, PCAT119, PCAT120, orPCAT121.
 22. The method of claim 20, wherein the sample is selected fromthe group consisting of tissue, blood, plasma, serum, urine, urinesupernatant, urine cell pellet, semen, prostatic secretions and prostatecells.
 23. The method of claim 20, wherein the nucleic acidamplification technique is selected from the group consisting ofpolymerase chain reaction, reverse transcription polymerase chainreaction, transcription-mediated amplification, ligase chain reaction,strand displacement amplification, and nucleic acid sequence basedamplification.
 24. The method of claim 20, wherein said cancer isselected from the group consisting of localized prostate cancer andmetastatic prostate cancer.
 25. A method of diagnosing and treatingprostate cancer in a subject, said method comprising: (a) obtaining asample from a subject, wherein the sample comprises non-coding RNAs(ncRNA)); (b) processing the sample to isolate or enrich the sample forncRNA or cells containing ncRNA; (c) detecting the level of expressionof one or more ncRNAs in said sample by sequencing, nucleic acidhybridization or nucleic acid amplification, wherein said one or morencRNAs is selected from the group consisting of one or more PCATs andSChLAP-1; (d) diagnosing the subject with prostate cancer when anincreased level of expression of said one or more ncRNAs in said samplerelative to the level in normal prostate cells is detected; and (e)administering an effective amount of a PARP inhibitor or radiation tothe diagnosed subject.
 26. The method of claim 25, wherein the PARPinhibitor is olaparib or ABT-888.
 27. The method of claim 25, whereinthe one or more PCATs is selected from the group consisting of PCAT1,PCAT2, PCAT3, PCAT4, PCAT5, PCAT6, PCAT7, PCAT8, PCAT9, PCAT10, PCAT11,PCAT12, PCAT13, PCAT14, PCAT15, PCAT16, PCAT17, PCAT18, PCAT19, PCAT20,PCAT21, PCAT22, PCAT23, PCAT24, PCAT25, PCAT26, PCAT27, PCAT28, PCAT29,PCAT30, PCAT31, PCAT32, PCAT33, PCAT34, PCAT35, PCAT36, PCAT37, PCAT38,PCAT39, PCAT40, PCAT41, PCAT42, PCAT43, PCAT44, PCAT45, PCAT46, PCAT47,PCAT48, PCAT49, PCAT50, PCAT51, PCAT52, PCAT53, PCAT54, PCAT55, PCAT56,PCAT57, PCAT58, PCAT59, PCAT60, PCAT61, PCAT62, PCAT63, PCAT64, PCAT65,PCAT66, PCAT67, PCAT68, PCAT69, PCAT70, PCAT71, PCAT72, PCAT73, PCAT74,PCAT75, PCAT76, PCAT77, PCAT78, PCAT79, PCAT80, PCAT81, PCAT82, PCAT83,PCAT84, PCAT85, PCAT86, PCAT87, PCAT88, PCAT89, PCAT90, PCAT91, PCAT92,PCAT93, PCAT94, PCAT95, PCAT96, PCAT97, PCAT98, PCAT99, PCAT100,PCAT101, PCAT102, PCAT103, PCAT104, PCAT105, PCAT106, PCAT107, PCAT108,PCAT109, PCAT110, PCAT111, PCAT112, PCAT113, PCAT114, PCAT115, PCAT116,PCAT117, PCAT118, PCAT119, PCAT120, or PCAT121.
 28. The method of claim25, wherein the sample is selected from the group consisting of tissue,blood, plasma, serum, urine, urine supernatant, urine cell pellet,semen, prostatic secretions and prostate cells.
 29. The method of claim25, wherein the nucleic acid amplification technique is selected fromthe group consisting of polymerase chain reaction, reverse transcriptionpolymerase chain reaction, transcription-mediated amplification, ligasechain reaction, strand displacement amplification, and nucleic acidsequence based amplification.
 30. The method of claim 25, wherein saidcancer is selected from the group consisting of localized prostatecancer and metastatic prostate cancer.
 31. A method of diagnosingprostate cancer in a subject, said method comprising: (a) obtaining asample from a subject, wherein the sample comprises non-coding RNAs(ncRNA)); (b) processing the sample to isolate or enrich the sample forncRNA or cells containing ncRNA; (c) detecting the level of expressionof one or more ncRNAs in said sample by sequencing, nucleic acidhybridization or nucleic acid amplification, wherein said one or morencRNAs is selected from the group consisting of one or more PCATs andSChLAP-1; and (d) diagnosing the subject with prostate cancer when anincreased level of expression of said one or more ncRNAs in said samplerelative to the level in normal prostate cells is detected.
 32. Themethod of claim 31, wherein the one or more PCATs is selected from thegroup consisting of PCAT1, PCAT2, PCAT3, PCAT4, PCAT5, PCAT6, PCAT7,PCAT8, PCAT9, PCAT10, PCAT11, PCAT12, PCAT13, PCAT14, PCAT15, PCAT16,PCAT17, PCAT18, PCAT19, PCAT20, PCAT21, PCAT22, PCAT23, PCAT24, PCAT25,PCAT26, PCAT27, PCAT28, PCAT29, PCAT30, PCAT31, PCAT32, PCAT33, PCAT34,PCAT35, PCAT36, PCAT37, PCAT38, PCAT39, PCAT40, PCAT41, PCAT42, PCAT43,PCAT44, PCAT45, PCAT46, PCAT47, PCAT48, PCAT49, PCAT50, PCAT51, PCAT52,PCAT53, PCAT54, PCAT55, PCAT56, PCAT57, PCAT58, PCAT59, PCAT60, PCAT61,PCAT62, PCAT63, PCAT64, PCAT65, PCAT66, PCAT67, PCAT68, PCAT69, PCAT70,PCAT71, PCAT72, PCAT73, PCAT74, PCAT75, PCAT76, PCAT77, PCAT78, PCAT79,PCAT80, PCAT81, PCAT82, PCAT83, PCAT84, PCAT85, PCAT86, PCAT87, PCAT88,PCAT89, PCAT90, PCAT91, PCAT92, PCAT93, PCAT94, PCAT95, PCAT96, PCAT97,PCAT98, PCAT99, PCAT100, PCAT101, PCAT102, PCAT103, PCAT104, PCAT105,PCAT106, PCAT107, PCAT108, PCAT109, PCAT110, PCAT111, PCAT112, PCAT113,PCAT114, PCAT115, PCAT116, PCAT117, PCAT118, PCAT119, PCAT120, orPCAT121.
 33. The method of claim 31, wherein the sample is selected fromthe group consisting of tissue, blood, plasma, serum, urine, urinesupernatant, urine cell pellet, semen, prostatic secretions and prostatecells.
 34. The method of claim 31, wherein the nucleic acidamplification technique is selected from the group consisting ofpolymerase chain reaction, reverse transcription polymerase chainreaction, transcription-mediated amplification, ligase chain reaction,strand displacement amplification, and nucleic acid sequence basedamplification.
 35. The method of claim 31, wherein said cancer isselected from the group consisting of localized prostate cancer andmetastatic prostate cancer.
 36. A method comprising: (a) obtaining asample from a subject, wherein the sample comprises non-coding RNAs(ncRNA); (b) processing the sample to isolate or enrich the sample forncRNA or cells containing ncRNA; (c) detecting the level of expressionof one or more ncRNAs in said sample by sequencing, nucleic acidhybridization or nucleic acid amplification, wherein said one or morencRNAs is selected from the group consisting of one or more PCATs andSChLAP-1; and (d) administering an effective amount of a PARP inhibitoror radiation to the subject based on the level of expression of one ormore ncRNAs in said sample.
 37. The method of claim 36, wherein the oneor more PCATs is selected from the group consisting of PCAT1, PCAT2,PCAT3, PCAT4, PCAT5, PCAT6, PCAT7, PCAT8, PCAT9, PCAT10, PCAT11, PCAT12,PCAT13, PCAT14, PCAT15, PCAT16, PCAT17, PCAT18, PCAT19, PCAT20, PCAT21,PCAT22, PCAT23, PCAT24, PCAT25, PCAT26, PCAT27, PCAT28, PCAT29, PCAT30,PCAT31, PCAT32, PCAT33, PCAT34, PCAT35, PCAT36, PCAT37, PCAT38, PCAT39,PCAT40, PCAT41, PCAT42, PCAT43, PCAT44, PCAT45, PCAT46, PCAT47, PCAT48,PCAT49, PCAT50, PCAT51, PCAT52, PCAT53, PCAT54, PCAT55, PCAT56, PCAT57,PCAT58, PCAT59, PCAT60, PCAT61, PCAT62, PCAT63, PCAT64, PCAT65, PCAT66,PCAT67, PCAT68, PCAT69, PCAT70, PCAT71, PCAT72, PCAT73, PCAT74, PCAT75,PCAT76, PCAT77, PCAT78, PCAT79, PCAT80, PCAT81, PCAT82, PCAT83, PCAT84,PCAT85, PCAT86, PCAT87, PCAT88, PCAT89, PCAT90, PCAT91, PCAT92, PCAT93,PCAT94, PCAT95, PCAT96, PCAT97, PCAT98, PCAT99, PCAT100, PCAT101,PCAT102, PCAT103, PCAT104, PCAT105, PCAT106, PCAT107, PCAT108, PCAT109,PCAT110, PCAT111, PCAT112, PCAT113, PCAT114, PCAT115, PCAT116, PCAT117,PCAT118, PCAT119, PCAT120, or PCAT121.
 38. The method of claim 36,wherein the sample is selected from the group consisting of tissue,blood, plasma, serum, urine, urine supernatant, urine cell pellet,semen, prostatic secretions and prostate cells.
 39. The method of claim36, wherein the nucleic acid amplification technique is selected fromthe group consisting of polymerase chain reaction, reverse transcriptionpolymerase chain reaction, transcription-mediated amplification, ligasechain reaction, strand displacement amplification, and nucleic acidsequence based amplification.
 40. The method of claim 36, wherein saidcancer is selected from the group consisting of localized prostatecancer and metastatic prostate cancer.